Overview
Choosing a payroll company is a high-stakes decision. It touches every paycheck, every tax filing, and every audit trail.
The right fit reduces risk and admin time. The wrong fit creates costly errors, penalties, and fire drills.
Even when you hire a third party, you remain responsible for payroll taxes and deadlines. Your selection criteria, verification steps, and go-live controls must be airtight. According to IRS Publication 15 (Circular E), employers are ultimately liable for employment taxes regardless of outsourcing. That frames this guide’s emphasis on pricing transparency, controls, and verification.
This buyer’s guide goes beyond listicles of “best payroll companies.” You’ll get total cost of ownership models, a phased implementation playbook, security and compliance checklists, integration guidance for QuickBooks, Xero, NetSuite, and Sage, and industry-specific workflows like certified payroll.
We also flag federal requirements you can’t ignore. That includes certified payroll reporting via U.S. Department of Labor Form WH-347 and 1095-C responsibilities and e-filing via the ACA Information Returns (AIR) Program. Use this to select, implement, and operate with confidence.
Transparent pricing and total cost of ownership
A fair price is more than a monthly sticker. Most payroll companies bundle a base platform fee, per-employee-per-month (PEPM) pricing, and optional add-ons. They then invoice separate fees for year-end forms and special processing.
If you only compare headline numbers, you’ll miss hidden charges that escalate costs over time. Normalize quotes using the same headcount, pay frequency, and add-on set. Model 12 months of operations, including peak events like year-end.
Beyond unit pricing, scrutinize contract details. Look at auto-renewals, price caps, and early termination language. Growth can increase both PEPM and form quantities. New jurisdictions or benefits can introduce additional filing and reconciliation fees.
Ask for a written breakdown of every fee you might encounter over a full year’s cycle. Bake that into your TCO.
Pricing components: base + PEPM + add-ons
Most proposals fall into predictable buckets you can compare apples-to-apples. Understanding these components helps you normalize quotes and avoid surprises.
A lean startup might only need core payroll. A 200-employee company with multi-state operations will layer in benefits, time, and integrations.
Common components to reconcile across vendors:
- Base platform fee: a monthly or annual charge (often tiered by headcount) for access to the system.
- PEPM charges: per-employee-per-month fees for active employees; sometimes separate PEPM for contractors.
- Pay run fees: per-payroll charges (less common in modern SaaS pricing but still encountered with legacy providers).
- Add-ons: time and attendance, benefits administration, 401(k) feeds, HRIS modules, and integrations.
- Form and filing fees: W-2/1099/1095 production, local tax filings, and amended returns.
- Professional services: implementation, data migration, custom reports, and GL mapping assistance.
Anchor your normalization on your exact pay frequency, expected turnover, headcount growth, and add-ons over the next 12 months. If you expect to add time tracking in Q3, include those costs for the months you’ll use it.
Hidden fees and TCO checklist
Headline price rarely includes everything. Garnishment administration, off-cycle runs, and year-end processing drive real dollars. Cancellation terms can add sting at exit.
Your TCO model should surface these line items early, not at renewal or year-end.
Watch for these common hidden fees and include them in your calculator:
- Year-end forms: W-2 ($3–$10 each), 1099-NEC/MISC ($2–$7 each), 1095-C ($1.50–$4 each).
- Amendments and corrections: W-2c, 941-X preparation/filing, and reprints.
- Garnishment processing: per-order, per-pay-period fees for child support or levies.
- Off-cycle and on-demand pay: per-run fees and funding cutoffs; EWA program fees if applicable.
- Implementation or migration: flat or hourly; may vary by complexity (multi-state, GL mapping).
- Integrations: 401(k) feeds, HSA/FSA connections, or premium accounting connectors.
- Cancellations: early termination fees or “form completion” charges if exiting before year-end.
To operationalize TCO, build a 12-month model with inputs for headcount, pay frequency, add-ons, turnover, and expected special processing. Add 10–15% contingency for growth or unplanned events. Examples include off-cycle bonuses and retro pay corrections. Request contractual caps on annual price increases.
Cost scenarios for 10, 50, and 200 employees
Putting real numbers to a year of service clarifies trade-offs. The ranges below reflect typical SaaS payroll companies in the U.S. with standard features and a moderate cadence of changes.
Your mix of add-ons, jurisdictions, and benefit feeds will shift results.
- 10 employees (semi-monthly, basic payroll + W-2s): Expect base plus PEPM of roughly $120–$260 per month ($60–$120 base plus $6–$14 PEPM). Year-end forms might run about $50 for 10 W-2s at ~$5 each and ~$8 for two 1099-NEC at ~$4 each. Plan for an occasional off-cycle run ($25–$50) and 1–2 garnishments ($5–$8 per pay period if applicable). Estimated annual TCO lands around $1,800–$3,400 including minor add-ons and year-end.
- 50 employees (bi-weekly, payroll + time + 401(k) feed + W-2/1095-C): Expect base plus PEPM of about $600–$1,150 per month ($90–$150 base plus $10–$20 PEPM). Year-end forms could be ~$300 for 50 W-2s at ~$6 each and ~$125 for 50 1095-C at ~$2.50 each. Add-ons often include time tracking ($2–$5 PEPM) and a 401(k) feed or API ($25–$100 per month). Implementation frequently ranges $500–$2,000. Estimated annual TCO is typically $9,500–$20,000 including add-ons and year-end.
- 200 employees (bi-weekly, multi-state, benefits admin + GL integration + ACA): Expect base plus PEPM of approximately $1,800–$4,000 per month ($200–$400 base plus $8–$18 PEPM). Year-end forms often total ~$1,500 (200 W-2s at ~$5 each plus 200 1095-C at ~$2.50 each). Common add-ons include benefits administration, advanced time and job costing, a NetSuite connector, and multiple 401(k) feeds. Professional services for implementation and cutover support typically run $3,000–$10,000. Estimated annual TCO is $25,000–$65,000+, driven by integrations, multi-state filings, and benefit complexity.
Use these as sanity checks against quotes. If your proposal is far outside these bands for a similar scope, ask for a detailed fee schedule and justification.
Payroll company vs PEO vs EOR
Payroll companies process your payroll under your EIN. Professional Employer Organizations (PEOs) enter a co-employment model and run payroll under the PEO’s EIN. Employers of Record (EORs) hire workers on your behalf in countries where you lack an entity and handle local payroll and compliance.
The right model hinges on your need for control, benefits scale, and international coverage. This is crucial in the 50–200 employee range, where complexity grows but you still need agility.
For U.S.-centric employers with established HR and benefits, a payroll company preserves control and direct employer status. PEOs can unlock large-group benefits and HR outsourcing but change legal relationships and reporting lines. EORs solve global hiring without a local entity, trading higher unit costs for speed and in-country compliance.
Clarify your priorities—cost, control, and compliance jurisdiction—before you evaluate vendors.
Decision criteria by risk, control, and compliance scope
Your decision should weigh liability appetite, the need for centralized control, and the breadth of compliance you expect the partner to shoulder. A mid-market firm might want PEO benefits leverage but balk at co-employment risk and reporting complexity.
An international expansion might make EOR the fastest path while you spin up entities.
Focus comparisons on:
- Control: Your EIN (payroll company) vs co-employment under PEO’s EIN vs EOR’s local entity.
- Risk allocation: Who signs and files which returns? How are tax notices handled and escalated?
- Benefits and HR scope: Health plan leverage, ACA reporting, and HR compliance guardrails.
- International footprint: Need for global onboarding, multi-currency pay, and local statutory benefits.
- Exit complexity: Unwinding co-employment or EOR assignments vs switching a payroll system.
Decide based on your 12–24 month roadmap. If you foresee significant M&A, entity changes, or cross-border hiring, pick the model that simplifies those moves. Avoid choices that lock you into friction.
Implementation timeline and migration
A disciplined implementation prevents payroll leaks and year-end rework. Most mid-market migrations take 6–10 weeks. Timelines vary with data quality, multi-state setup, benefits complexity, and integration scope.
Break work into phases: data collection and mapping, configuration, validation, parallel runs, and go-live. Set explicit acceptance criteria at each gate. Align your cutover to a quarter boundary where possible to simplify tax balancing and reporting.
Treat implementation like a mini-audit. Verify employee master data, taxes, benefits, and GL mappings before you run money. Use parallel runs to compare outputs line by line and resolve variances before paychecks or filings hit. Freeze policy changes during parallel testing to avoid chasing a moving target.
Data mapping checklist and acceptance criteria
Clean inputs drive clean payroll. Map every data element from your current system. Confirm the new system’s fields and calculation rules produce the same net pay, taxes, and employer costs for the same inputs.
Acceptance criteria should be numeric and binary, not “looks good.”
Data to gather and map:
- Employee and tax profiles: names, addresses, SSNs, work locations, resident states, SUI rates, localities, reciprocity.
- Pay and history: pay rates, schedules, FLSA status, YTD/QTD wages and taxes, PTO balances.
- Deductions and benefits: medical/dental/vision elections, 401(k)/HSA/FSA types and limits, arrears handling, employer contributions.
- Earnings and codes: regular, OT, double-time, shift differentials, tips, bonuses, job costing dimensions.
- GL structure: chart of accounts, departments/classes/locations/projects, segment rules for mapping wages, taxes, and liabilities.
Define acceptance criteria such as: “For 20 sampled employees across all scenarios, net pay matches prior system within $1 and each tax or deduction matches to the penny. Employer tax liability per pay period ties to expected totals. GL export posts without out-of-balance entries.”
Only move forward when these pass.
Parallel runs, reconciliation, and cutover calendar
Parallel runs are your safety net. Run at least two cycles in parallel, feeding the same hours and compensation. Reconcile gross-to-net, employer taxes, and GL postings.
Investigate any variance, including rounding rules, overtime calculations, or benefit accruals. Resolve root causes before go-live.
Build a cutover calendar that includes:
- Final data freeze and YTD/QTD import.
- First and second parallel payroll dates and reconciliation windows.
- Bank verification, funding tests, and prenotes if needed.
- First live payroll submission cutoff and approval checkpoints.
- Post-go-live “hypercare” period for same-day corrections and support escalation.
Balance QTD/YTD totals to the penny against prior 941s and internal ledgers before you file under the new system. Document acceptance and keep an audit trail.
Switching providers mid-year
Mid-year switching is feasible with tight controls and a realistic timeline. The safest windows are the start of a quarter (Q2, Q3, Q4). These align with Form 941 periods and simplify reconciliation.
The core risks are misaligned YTD amounts, duplicated or missed filings, and W-2 errors. Those can cascade into employee tax headaches. Define who files what for each quarter, get that in writing, and run a W-2 preview in the fall to detect issues early.
Clarify amended return responsibilities in your termination and new service agreements. If the outgoing provider owes filings or corrections, hold them to dates and obtain proof of submission.
Regardless of vendor responsibilities, employers remain liable for taxes and filings per IRS Publication 15 (Circular E). Maintain oversight and retain confirmations.
W-2 continuity and QTD/YTD reconciliation
Accurate W-2s depend on clean YTD wages and taxes. Decide whether the new provider will consolidate a single W-2 for the year or if employees will receive two W-2s. A single W-2 is cleaner for employees but demands perfect YTD imports and reconciliation.
Use this approach to avoid errors:
- Import and verify YTD/QTD amounts for each tax type (federal, state, local, Social Security, Medicare) and each earning or deduction code.
- Tie cumulative wages and withholdings to prior 941s and state returns; reconcile FUTA credit and SUI wage bases.
- Run a W-2 preview in November. Confirm Box 1 vs pre-tax deductions, Boxes 3–6 Social Security and Medicare wages and taxes, and state and local boxes.
- Lock down final payrolls and year-end adjustments with clear ownership for any W-2c issuance.
Keep a reconciliation workbook with employee-level tie-outs and totals by jurisdiction. It becomes your defense file if questions arise at year-end.
Security and privacy essentials
Payroll systems hold SSNs, bank accounts, and wage data. That makes them prime targets.
Demand verifiable controls such as SOC 2 Type II and ISO/IEC 27001 certifications. Require strong encryption at rest and in transit, enforced SSO and MFA, granular RBAC, and immutable audit logs. Review independent reports, not just marketing claims. Confirm the scope includes the exact systems that store and process your data.
Standards matter because they codify the controls you expect. SOC 2 evaluates security, availability, and confidentiality under the AICPA’s Trust Services Criteria. ISO/IEC 27001 certifies a mature information security management system.
Ask for current reports and management responses to any exceptions. Verify authenticity via the issuers (AICPA SOC 2, ISO/IEC 27001 Information Security Standard).
Identity, access, and audit
Identity and access hygiene reduces the blast radius of mistakes and breaches. Your payroll company should support SSO (SAML/OIDC), enforce MFA, and allow least-privilege roles. Segregate duties across payroll processing, approvals, and banking.
Regular role reviews ensure that ex-employees and role changes don’t leave toxic combinations in place.
Expect:
- SSO/MFA enforcement and SCIM provisioning to automate joiner/mover/leaver updates.
- Granular RBAC with maker-checker workflows for payroll approvals and bank changes.
- Immutable audit logs of logins, config changes, and pay runs with retention aligned to your compliance needs.
- Encryption at rest (e.g., AES-256) and in transit (TLS 1.2+) and controls over data residency and backups.
Confirm that administrators cannot disable logging or approve their own changes without a second approver. Ask to see an example audit trail for a pay run and a bank account change.
Regulatory credentials and how to verify them
A credible payroll partner should prove its regulatory status and e-file capabilities. Look for participation in the IRS Reporting Agent Program, SSA Business Services Online credentials for W-2 e-file, and state e-file approvals where you operate.
Verification goes beyond logos. Ask for evidence and walkthroughs of the exact filing pathways they will use for you.
Get a demonstration of authorization flows. Include how your Form 8655 (Reporting Agent Authorization) will be executed and stored. Ask how the provider monitors agency notices and rejects.
For SSA and state portals, request proof of enrollment and sample submission confirmations (with sensitive data redacted). You want end-to-end traceability.
Who is liable for payroll taxes?
Employers are liable for payroll taxes and filings even when a third party calculates and remits them. The IRS is clear: using a payroll service does not transfer ultimate responsibility.
Your controls and oversight cannot be “outsource and forget.” Set agency authorizations properly, monitor cash withdrawals, and reconcile filing confirmations.
Reduce risk with:
- Executed Form 8655 tied to the provider’s Reporting Agent ID and scope defined.
- EFTPS enrollment under your business with email and text alerts for withdrawals.
- A monthly review of tax liability reports against cash debits and agency confirmations.
- Documented roles for who files 941/940 and state returns each period.
Review IRS Publication 15 (Circular E) for responsibilities and keep a compliance calendar you control. Your oversight is the last line of defense.
Integrations, APIs, and general ledger mapping
Tight integrations and clean GL mapping are where payroll time savings materialize. Evaluate native connectors to QuickBooks Online, Xero, NetSuite, and Sage. Confirm support for major time systems.
Test APIs and webhooks in a sandbox before buying. The goal is repeatable, reconciled flows that reduce manual journal entries and month-end churn.
Ask vendors to demonstrate end-to-end. Start with hours importing from time, gross-to-net calculation, and tax postings. Finish with a GL export into your accounting system, segmented by department, class, or location.
Validate error handling. What happens when an account is missing, a dimension is invalid, or an employee transfers mid-pay period?
Accounting/time integrations and data flow
Data should move securely and predictably. Most modern connectors use OAuth for authentication. They support daily or on-demand syncs and surface exceptions you can fix without re-running payroll.
For time systems, ensure earnings codes and overtime rules map correctly to payroll earnings.
Confirm:
- Authentication: SSO/OAuth for accounting and time systems; least privilege app scopes.
- Sync cadence: scheduled and manual triggers, with status dashboards and retry logic.
- Exception handling: clear error messages when accounts or dimensions are missing, with links to fix and re-post.
- Idempotency: re-running a failed post won’t duplicate entries in the GL.
- Change management: versioning of earnings codes and mappings to prevent silent drift.
Request a sandbox walkthrough that shows a failed post, a correction, and a successful repost to verify resilience.
GL mapping, dimensions, and reconciliation
GL mapping should mirror your reporting needs, not force you into one-size-fits-all. Segment wages, taxes, and employer contributions by department, class, location, project, or job code. This powers profitability and budget variance analysis.
Good setups eliminate manual reclasses and speed month-end close.
Use this approach:
- Define a mapping matrix that assigns each earning, tax, and deduction to a GL account and dimension set.
- Separate liability accounts for federal, state, and local taxes; benefits; and garnishments.
- Post summary-level entries per dimension to fit your close cadence while preserving detail in payroll reports.
- Reconcile: tie posted journal totals to payroll register totals and cash disbursements; investigate discrepancies immediately.
Lock the mapping after sign-off and document change control. A stable GL bridge is a major source of ROI.
Multi-state payroll, global coverage, and industry-specific workflows
Remote teams and growth introduce multi-state intricacies and local tax filings. Payroll companies should handle reciprocity rules, assign correct SUI rates and local taxes, and generate locality filings where required.
If you operate internationally, decide whether you need a payroll company with global modules, a network of local partners, or an EOR. An EOR can employ in-country until entities are established.
Industry workflows can be make-or-break. Construction may require certified payroll with prevailing wage, fringe benefits, and job-class detail. Manufacturing and professional services may need robust job costing. Hospitality has tip credit, pooled tips, and service charge nuances. Nonprofit and church payroll can involve clergy housing allowance and FICA exceptions.
Bring these needs into discovery so they’re configured and tested before go-live.
Certified payroll and prevailing wage
Government-funded construction projects often require weekly certified payroll reporting using U.S. Department of Labor Form WH-347. Your provider must track job classifications, base rates, fringe benefits, and hours by project to generate compliant reports.
Errors here jeopardize contract compliance and payments.
Confirm the system can:
- Capture project, classification, and fringe detail on each timesheet or earning line.
- Produce WH-347 with signatory certification and retain weekly archives.
- Support union dues, apprenticeship ratios, and job cost allocations for burdened labor.
Test with a real project’s data and compare outputs to your current compliance reports before go-live.
Pay options and benefits-related deductions
Pay flexibility improves employee experience and retention. Direct deposit is standard. Pay cards and earned wage access (EWA) add options for unbanked workers or those needing early access.
Benefits deductions (401(k), HSA/FSA, garnishments, COBRA) require precise setup and reconciliation. That avoids tax and ERISA errors. For COBRA continuation coverage specifics, consult U.S. Department of Labor COBRA and confirm your provider’s administration model.
Ensure payroll and benefits systems agree on deduction limits, employer matches, and arrears policies. Reconcile feeds to carriers and recordkeeper files each cycle, especially during open enrollment and high turnover periods.
Pay cards and earned wage access: fees and compliance
Alternative pay methods should be employee-friendly and lawful. Many states require a no-cost option to access full wages and prohibit forcing pay cards.
EWA programs vary in structure and fees. Some jurisdictions are tightening oversight of tips and advances.
Evaluate:
- Employee consent and opt-out: written disclosures and alternative pay options.
- Fees: ATM access, inactivity, replacement cards, EWA transaction fees; ensure clear disclosures.
- Funding and settlement: cutoffs, failed deposit handling, and chargeback risk allocation.
- State considerations: tip credit interactions, final pay rules, and restrictions on deductions.
Pilot with a small cohort and monitor adoption, fees, and support tickets before broad rollout.
Year-end processes and ongoing operations
Year-end is not a single event; it’s a project that spans November to January. Your payroll company should guide W-2, 1099, and 1095 production. They should offer pre-publication previews and manage e-file pathways through SSA and the IRS AIR system where applicable.
Good operations maintain an audit trail for every correction and reprint. They also keep records for multiple years in accessible formats.
Establish a year-end timeline with checklists for address updates and fringe benefits (e.g., GTL imputed income). Include bonus withholding and final adjustments. Run test files for carriers and agencies where supported.
Notify employees early about digital vs paper forms and availability dates.
Amendments, corrections, and reprints
Corrections are inevitable; how they’re handled matters. W-2c and 1095-C corrections must flow through to amended returns (e.g., 941-X) when appropriate.
Your provider should retain both the original and corrected filings with timestamps and reason codes. Reprints should be self-service for employees where possible, with employer controls for re-issuance.
Set expectations for:
- SLA on corrections (e.g., within 10 business days of request).
- Who pays amendment and refiling fees and in what scenarios.
- How employees are notified of corrected forms and where to access them.
- Retention policies for forms, filings, and audit logs aligned to your compliance program.
Proactive W-2 previews and reconciliation against quarterly filings reduce last-minute surprises and rework.
Service levels, support model, and due diligence
Payroll is time-sensitive, so service levels must be explicit. Expect uptime targets (e.g., 99.9%), documented maintenance windows, and SLAs for first response and resolution across channels (chat, email, phone).
Clarify whether you get a dedicated payroll specialist or a pooled support model. Map the escalation path when payroll is at risk.
Due diligence extends beyond go-live. Review data retention and deletion policies, export rights, and exit support terms before you sign. Confirm the provider’s disaster recovery posture (RTO/RPO). Ask how incidents are communicated and remediated.
Your contract should turn these expectations into measurable obligations.
Risk controls and exit planning
Avoid lock-in by structuring your data and your contract for portability. If you ever need to switch, you’ll want all payroll history, filings, and GL references in standard formats you can load elsewhere.
Exit planning is not pessimism; it’s prudent governance.
Build this into your contract and operations:
- Data export rights: full employee and payroll history, filings, and audit logs in CSV/PDF; API access during wind-down.
- File formats and schemas: documented GL export structure, time and earnings code dictionaries, and mapping files.
- Sunset timeline: how long post-termination you retain portal access and how year-end forms will be handled.
- Notice periods and fees: clear early termination terms and form completion charges if exiting mid-year.
- Security at exit: data deletion certificates and confirmation of backup retention policies.
Do a quarterly restore test of your own exports to confirm you can reconstitute critical records if needed.
ROI evidence and benchmarking
Payroll ROI is time saved, errors avoided, and penalties prevented—not just lower software fees. Baseline your current state before you switch. Track hours per payroll cycle, manual journal entries, and error rates (adjustments per 1,000 payslips). Include the number of agency notices and time to close payroll-related GL accounts.
Post-implementation, measure the same KPIs. Attribute improvements to specific features or process changes.
Build a simple ROI model that credits:
- Cycle time reduction (hours saved x fully loaded wage rate).
- Error reduction (rework hours avoided + reduced over or underpayments).
- Fewer agency notices and penalties (direct dollars + admin time).
- Faster month-end close (earlier visibility for decision-making).
- Improved compliance coverage (quantified risk reduction where feasible).
Use these benchmarks in QBRs with your provider to drive continuous improvement. Tie SLA performance to renewals.
Vendor RFP checklist and next steps
A structured RFP keeps you in control and drives meaningful demos instead of generic slides. Weight criteria to reflect your risks and goals. Script scenarios for the demo and ask reference customers targeted questions.
Verify credentials and certifications via authoritative sources like AICPA SOC 2, ISO/IEC 27001, the IRS Reporting Agent Program, and SSA Business Services Online.
Use a weighted scoring model:
- Pricing and TCO (25%): normalized base + PEPM + add-ons, year-end, implementation, and cancellation terms; price caps and renewals.
- Compliance and security (25%): SOC 2 Type II, ISO 27001, encryption, SSO/MFA, RBAC, audit logs, data residency, incident response.
- Integrations and APIs (20%): native connectors to QuickBooks/Xero/NetSuite/Sage, time systems; GL mapping flexibility; API/webhook quality and sandbox.
- SLAs and support (15%): uptime, first-response/resolve times, dedicated rep vs pooled, escalation path, maintenance windows.
- Industry and complexity fit (15%): multi-state/locality filings, ACA/1095-C/COBRA, certified payroll/union/job costing, hospitality tips, nonprofit/church nuances.
For the demo script, ask vendors to:
- Run a parallel payroll scenario with multiple states, a garnishment, and a bonus.
- Import hours from your current time system and show exception handling.
- Map earnings, taxes, and deductions to your GL dimensions and post to your accounting sandbox.
- Preview W-2/1095-C outputs and walk through a correction and reprint.
- Show audit logs for a bank account change and a payroll approval workflow.
Reference checks to run:
- How quickly did implementation achieve stable, error-free runs? What slipped and why?
- How often do agency notices occur, and how does the vendor handle root cause and remediation?
- What is real-world first response and resolution time during payroll week?
- How clean are the GL postings and how much manual cleanup remains?
- Has the customer executed a mid-year switch with this vendor and how did W-2s play out?
Next steps: shortlist 3–4 payroll companies and issue the RFP with your weighted criteria and demo script. Verify credentials via the authoritative sources above and schedule a pilot or parallel-run proof for your most complex scenario.
Align your internal timeline to a quarter boundary. Enforce acceptance criteria that tie directly to risk, cost, and accuracy. With that discipline, you’ll choose a partner that not only runs payroll, but also strengthens your financial controls and employee trust.