Does Paychex do certified payroll?

Not in Paychex Flex itself. Paychex's certified payroll article (June 2026) describes the payroll records a certified payroll is built from and does not describe a WH-347 report in Flex. Points North's integration reads Paychex Flex and produces the federal and state forms, priced by agreement. Any Paychex account can export the journal, which is enough to build the form here.

We have certified payroll through a Paychex integration. 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.

Your payroll system

Certified payroll from Paychex Flex: the integration route, the payroll journal, and what to check

Paychex Flex has no WH-347 of its own; certified payroll comes through an integration such as Points North, or from the payroll journal every account can export. What each route gives you, how the columns land on the WH-347, and what a reviewer checks either way.

Checked against the sources below October 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 Flex does not print a WH-347 or a Statement of Compliance. Paychex's own certified payroll article describes the payroll records behind the report, and the report itself comes from an integration: Points North connects to Paychex Flex and produces the federal WH-347 and state formats, priced by agreement with Points North. 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, which is enough to build the form here. Whichever route you take, the figures 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, and Custom Reporting, which picks the fields and downloads as a spreadsheet.
Multiple pay rates and job codes when your representative sets them up, so hours can be paid by classification.
An integration route to certified payroll: Points North reads Paychex Flex and produces the WH-347 and state formats; its price is set in your Points North agreement.

What the WH-347 still needs

In Paychex Flex itself: the WH-347, the wage determination number, determination-worded classifications, the fringe split and the Statement of Compliance.
Through an integration: 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 a report with only the columns you need.
Set the date range to the pay period for the week you are certifying.
Download it and save it as CSV if it is not one already. Column names vary by report and setup; the ones below are typical, and the import's mapping step lets you point any column at the right field.

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 # (typical)	Matched to the crew by name; the employee number becomes the identifying number when the crew record has none.
Reg Hours, OT Hours (typical)	Straight time spread across the week; overtime as Paychex split it.
Rate	Column 6A, checked against the determination.
Gross	Compared with rate × hours: equal sets the cash fringe to 0; a plausible excess becomes the cash fringe per hour; a gross far past that is kept as 7B.
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 you go through an integration, that setup drives its report; if not, it is what makes the export map cleanly.

Fringe

Cash in lieu goes through an earnings code paid per hour, which lifts the gross above rate × hours; the import sets the difference per hour as the cash fringe. 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 (or as Excel, saved as 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?: Not in Paychex Flex itself. Paychex's certified payroll article (June 2026) describes the payroll records a certified payroll is built from and does not describe a WH-347 report in Flex. Points North's integration reads Paychex Flex and produces the federal and state forms, priced by agreement. Any Paychex account can export the journal, which is enough to build the form here.
We have certified payroll through a Paychex integration. 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.

Sources

Keep Paychex Flex. Add the form.

Export the week, import it, read the checks, file. The WH-347 and the signed statement print; the prime gets the PDF. Free for one payroll a month, $19 for unlimited.

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