Certified payroll from Paychex Flex: the payroll journal, the certified payroll add-on, and what to check
Some Paychex service levels include a certified payroll report; the rest export a payroll journal with hours and deductions. What each gives you, how the columns land on the WH-347, and what a reviewer checks either way.
Checked against Paychex Flex’s help center September 16, 2026. Menus move; if a step is off, tell us from the Help menu and it is fixed the same week.
The short answer
Paychex offers certified payroll reporting on some service plans and through its Points North integration, and every Paychex Flex account can export a payroll journal or a custom report with hours, rates, gross, federal withholding, Social Security and Medicare per employee. Whether you use Paychex's form or import the journal here, the numbers that get payrolls rejected are the same: the classification wording, the fringe columns and the overtime base.
What Paychex Flex gives you
- A payroll journal and check register for any pay period, plus a custom report builder that can select every field (choose All Fields under Layout) and export to CSV.
- Multiple pay rates and job codes when your representative sets them up, so hours can be paid by classification.
- A certified payroll report on some plans, built from job codes, worker classifications and wage determinations you configure before running payroll.
What the WH-347 still needs
- On plans without the certified payroll report: the wage determination number, determination-worded classifications, the fringe split and the Statement of Compliance.
- On plans with it: nothing structural, but the report is only as right as the job codes and rates configured behind it, and a reviewer sees the result, not the setup.
The export: Payroll Journal (or a custom report)
- Reports (Analytics & Reports in Flex), then Payroll Journal, or Custom Reporting to build one with only the columns you need.
- Set the date range to the pay period for the week you are certifying.
- Export as CSV. In Custom Reporting choose All Fields under Layout if you are not sure what to include.
How each column lands on the form
The import matches columns by meaning, so the exact header can vary. It asks about anything it is unsure of before it fills the grid.
| In Paychex Flex | On the certified payroll |
|---|---|
| Employee, Emp # | Matched to the crew by name; the employee number becomes the identifying number when the crew record has none. |
| Reg Hours, OT Hours | Straight time spread across the week; overtime as Paychex split it. |
| Rate | Column 6A, checked against the determination. |
| Gross | Used to work out whether fringe was paid as cash. |
| Fed W/H | Column 8, withheld. |
| Soc Sec, Medicare | Column 8, FICA, added together. |
Rates and classifications
Ask your representative to set up a job code per classification with the determination's wording. If your plan includes the certified payroll report, that setup is what drives it; if not, it is what makes the export map cleanly.
Fringe
Cash in lieu goes through an earnings code paid per hour. Plan contributions are the employer's per-hour cost, recorded in CertifiedHours against the plan; Paychex's benefit deductions are the worker's share and do not count toward the fringe.
Every week
- Run payroll in Paychex Flex as usual, with the workweek ending on the day your contract's payroll week ends.
- Export the payroll journal for that pay period as a CSV.
- Open the week in CertifiedHours and choose Import hours from CSV. The columns are matched by meaning; check the two or three it asks about.
- Read the grid once against the export: trades, hours, rates, the fringe line. Fix anything the checks flag.
- File. The WH-347 and the signed Statement of Compliance print, and the prime gets the PDF by email if the job is set to send.
Questions people ask
- Does Paychex do certified payroll?
- On some service levels, yes, and through the Points North integration on others. Ask your representative which your plan includes and what it costs. Any plan can export the journal, which is enough to build the form elsewhere.
- We have the Paychex certified payroll report. Why would we also use this?
- You may not need to. Contractors who do use it for the checks before signing (rates against the determination, 7B never under 7A, fringe on every hour), for the sends to the prime with a record, and for the LCPtracker file.
- Which Paychex number goes in column 1E?
- The employee number. It is consistent week to week and is not part of the Social Security number.