Labor booked as one lump
When every paycheck flows into a single wages account, you cannot see what any job paid in labor. Your biggest cost becomes invisible at exactly the level where you need it most.
Comparison guide
Payroll for Contractors: Which Processor Fits, and How the Books Stay Clean
Running payroll is one decision. Getting that payroll into your books correctly is a completely separate one. Most contractors pick a processor and call it done, then wonder why their job margins look wrong. The processor cuts checks. Your books are where the labor has to land, job by job, with burden tracked and W-2 crews separated from 1099 subs. This page covers both: how the main processors compare for contractor use, and how we handle the bookkeeping side inside your QuickBooks Online file.
Quick answer
- Labor is usually your largest job cost. Every paycheck needs to land on the right job in your books, not in one company-wide wages line.
- Your payroll processor cuts checks and files taxes. We handle the bookkeeping: mapping each pay run to the correct job, recording burden, and reconciling into your monthly close.
- W-2 field crews and 1099 subcontractors are tracked in distinct streams all year. January is a confirmation, not a scramble.
- Certified payroll recordkeeping is supported on prevailing-wage and public-works jobs where your contracts require it.
- Payroll bookkeeping is included on the Shop plan and up.
What contractor payroll actually needs from a processor
Most payroll processors were built for offices. A contractor has a different checklist. You need to pay W-2 field crews, track 1099 subcontractor payments for 1099-NEC filing, handle workers compensation classifications, and support multi-state payroll if crews cross state lines. On public-works jobs, you may need certified payroll reports.
None of the processors below do your bookkeeping for you. They cut checks and file payroll taxes. The job-costing of wages, the recording of burden (employer taxes, workers comp, benefits), and the reconciliation into your monthly close all happen on the bookkeeping side. That is where we come in, regardless of which processor you run.
- W-2 employee payroll with full-service tax filing and deposits
- 1099 subcontractor payment tracking and 1099-NEC e-file
- Workers compensation classification support
- Multi-state payroll for crews who work across state lines
- Certified payroll reporting support for prevailing-wage jobs (not all processors)
- QuickBooks Online integration for bookkeeping reconciliation
Payroll processors compared for contractors (June 2026)
Prices change frequently. The figures below were verified on each provider's own pricing page in June 2026. Always confirm the current rate at the provider's site before signing up.
| Provider | Pricing (as of June 2026) | QuickBooks sync | Certified payroll | Multi-state | 1099 and contractor pay |
|---|---|---|---|---|---|
| GustoContractor-only plan ($6/person, no base fee) pays 1099 contractors only, no W-2 employees. Job costing and class exports available on Plus and up. | Contractor-only: $0 base + $6/person. Simple: $49/mo + $6/person. Plus: $80/mo + $12/person. Premium: $180/mo + $22/person. | Yes, all plans | Premium plan only | Available | Yes, 1099-NEC e-file |
| QuickBooks PayrollNatively syncs with your QBO file with no export step. "Track project profitability" is listed on the Workforce Premium + Plus tier. Pricing page shows bundles only; standalone payroll add-on pricing requires sign-in or call. | Sold in bundles with QuickBooks Online accounting. Workforce Payroll + Simple Start: $88/mo + $6.50/person. + Essentials: $125/mo + $6.50/person. Workforce Premium + Plus: $203/mo + $10/person. If you already have QBO, add payroll separately (see provider for current add-on price). | Native (same platform) | Not listed in standard plan features. See provider. | Yes | Yes, 1099 e-file included |
| ADP RUNWidely used by contractors at larger crew sizes. Pricing requires a sales call. | Custom quote. No public pricing. Four plans: Essential, Enhanced, Complete, HR Pro. Contact ADP for a rate. | Yes | Available (confirm with provider) | Yes | Yes, 1099 forms |
| SurePayrollLower base price than Gusto or QuickBooks Payroll. QBO sync is an add-on, not included. Geared toward general small business, not trade-specific. | $29/mo base + $7/worker/mo. Multi-state: add $9.99/mo. Accounting software integration (includes QuickBooks): add $4.99/mo. | Yes, as a paid add-on ($4.99/mo) | Not listed on pricing or features pages. See provider. | $9.99/mo add-on | Yes, 1099-NEC filing available |
| Square PayrollStraightforward pricing. Multi-state only on full-service. No mention of certified payroll or prevailing wage. Good fit for smaller crews already using Square for payments. | Full-service (W-2 + 1099): $35/mo + $6/person paid. Contractor-only (1099 only, no W-2): $6/person paid, no base fee. | Yes, QBO Online integration included | Not listed. See provider. | Full-service plan only | Yes; contractor-only plan available |
| PaychexFrequently used by mid-sized contractors. Certified payroll support confirmed. Pricing requires a sales contact. | Custom quote. No public pricing. Contact Paychex for a rate. | Yes | Yes (confirmed on site) | Yes | Yes, 1099 forms |
What the processor does vs what the bookkeeping does
The processor runs the payroll: it calculates wages, withholds taxes, deposits employer and employee taxes, cuts direct deposits, and files quarterly and annual tax forms. That is a full-service function and worth having done professionally.
The bookkeeping is a separate layer. The processor tells you what you paid in total. It does not tell you that the Henderson job ran over on labor while the Miller job came in under. That visibility only exists when each pay run is mapped to the correct job inside your QuickBooks file, with employer taxes and burden recorded alongside the wages.
Our job is that second layer. We take your payroll processor exports, reconcile them into your QuickBooks Online file every month, map wages to the correct job using Class or Location tracking, and make sure the burden lands on the job, not in a corporate overhead account. The result is a monthly close where your labor numbers are real and your job margins are not fiction.
- Your payroll processor files taxes and cuts checks. We book those figures into QBO with job-level allocation.
- Every pay run reconciles against your bank in the monthly close so the books and the processor agree.
- Employer payroll taxes and workers comp burden are recorded to each job, not to a single overhead line.
- W-2 wages and 1099 sub payments flow through separate accounts so your labor reporting and sub totals stay clean.
- For prevailing-wage jobs, we maintain the job-costed wage records that certified payroll reporting is built from.
Which processor is the best fit for contractors
There is no single right answer. The fit depends on your crew size, whether you cross state lines, whether you have prevailing-wage work, and whether you already use QuickBooks Online.
If you already run QuickBooks Online, the native integration in QuickBooks Payroll removes an export step, though the bundled pricing means you are paying for QBO and payroll together. Gusto has a clean interface and a lower entry price for small crews; certified payroll is on the Premium tier. ADP RUN and Paychex are built for scale and both have certified payroll support, but require a quote. SurePayroll and Square are worth a look for straightforward small crews that do not need certified payroll.
What none of them do is manage your bookkeeping. That part, the job-costing of labor, the burden tracking, and the monthly reconciliation, is what we handle on the Shop plan and up, regardless of which processor you choose.
Where contractor payroll bookkeeping usually goes wrong
Burden ignored
Employer payroll taxes, workers comp, and benefits can add a real percentage on top of base wages. Leave them out of job cost and your true labor cost per job is understated, so your margins look stronger than they are.
Subs mixed in with payroll
Running 1099 subcontractors through the same bucket as W-2 wages loses both your labor numbers and your 1099 totals, turning January into a reconstruction project.
Processor and books never reconcile
If your payroll processor total and your QuickBooks payroll expense never match, you cannot trust either number. The gap is often buried in employer tax timing or a missed burden entry.
Which plan includes payroll bookkeeping
- Truck, solo operator, 1 to 2 accounts, simple job tracking
- Crew, growing crew, job costing, FSM sync included
- Shop, payroll, 1099 subs, AR/AP, priority close
- Builder, multi-entity, high volume, custom mapping
Contractor payroll FAQ
Do you run payroll, or just book it?
We handle the bookkeeping side. Payroll runs through your payroll processor, and we manage the QuickBooks side: mapping each pay run to the correct jobs, recording payroll taxes and burden, and reconciling the processor against your QBO file every month. You keep your processor and your filings. Payroll bookkeeping is included on the Shop plan and up.
Which payroll processor should I use as a contractor?
It depends on your situation. If you already run QuickBooks Online, QuickBooks Payroll has a native integration that removes an export step. Gusto is a common choice for smaller crews with a clean interface and transparent pricing. ADP RUN and Paychex both support certified payroll and are built for larger crew sizes but require a custom quote. SurePayroll and Square are lower-cost options for straightforward small crews. We reconcile payroll from any processor into your QuickBooks file, so the choice is yours.
Can you job-cost our labor?
Yes. We map each pay run to each job using Class or Location tracking in QuickBooks. Wages, employer payroll taxes, and burden land against the job they belong to. That is what lets you see real labor cost and gross profit by job, rather than a single company-wide wages figure.
Do you support certified payroll?
For prevailing-wage and public-works jobs, we maintain the job-costed wage records that certified payroll reporting is built from and support the process where your contracts require it. Certified payroll reporting formats and wage determinations vary by jurisdiction, so we coordinate with you and your payroll processor on the specifics. The bookkeeping foundation, accurate wages and hours tied to the correct job, is what makes certified payroll reporting possible.
Which payroll processors support certified payroll?
Based on published features as of June 2026: Gusto supports certified payroll on its Premium plan. Paychex confirms certified payroll support on its site. ADP RUN offers certified payroll as part of its service (contact for plan details). QuickBooks Payroll, SurePayroll, and Square do not list certified payroll as a standard feature. Verify current capabilities with each provider before committing.
How do you keep W-2 employees and 1099 subs separate?
They run in distinct streams all year. W-2 wages flow through payroll and into job costing as direct labor. Subcontractor payments are tracked separately, with W-9s collected at engagement and running payment totals maintained through the year. Keeping them apart protects both your labor reporting and your 1099 filing so neither becomes a year-end scramble.
Which plan includes payroll bookkeeping?
Payroll handling is part of the Shop plan and up, alongside 1099 subcontractor tracking and AR/AP tracking. The Truck and Crew plans focus on core bookkeeping and job costing. If you are not sure which plan fits your crew size and payroll needs, head to the get-started page and we will scope it with you.
Does SurePayroll integrate with QuickBooks?
Yes. SurePayroll offers accounting software integration, which includes QuickBooks, as a paid add-on at $4.99 per month as of June 2026. Confirm current pricing and supported QuickBooks versions at surepayroll.com.
Payroll that lands on the right job, every month
Trade-native categories, job costing, and an expert-reviewed close every month. You keep your QuickBooks file.