How to Create a Positive Pay File From Paychex
Paychex Flex does not export a positive pay file. No menu item produces a check issue file in your bank's format, and the payroll exports Paychex does offer are built for your general ledger, not for bank fraud control. To meet a positive pay requirement, you pull your payroll check data out of Paychex Flex, then convert it into the layout your bank expects. This guide shows which report to use and how to convert the export for free.
If positive pay is new to you, read what is positive pay first. In short, your bank matches each check that clears against a list of checks you issued, by check number, amount, and issue date. Anything that does not match gets flagged. That list is the positive pay file.
Only paper paychecks belong in the file
Positive pay protects physical checks that someone could counterfeit or alter. Direct deposit pays do not produce a check that clears the same way, so they do not belong in the file. If only a few employees get a printed paycheck, your file should contain only those checks. Before you export, know which payments in a run were paper checks versus direct deposits.
Step 1: Run the report in Analytics & Reports
Paychex Flex keeps reports in the Report Center. From the dashboard, go to Dashboard > Analytics & Reports, then choose View All Reports. The report you want is the Payroll Journal, which Paychex generates automatically for every payroll and which lists each employee's pay detail, including net pay and check or voucher numbers. The Cash Requirements report is a useful companion that itemizes the net amounts paid out. Open the report, set the date range, and run it. If fields are missing, use Create Report to add columns such as check number, net pay, and check date.
Step 2: Export to Excel or CSV, not PDF
Paychex Flex offers a View in browser option and a set of Download as radio buttons, or an export icon, with formats that include Microsoft Excel (XLS / Excel 2007+), CSV, XML, and PDF. Choose Excel or CSV. Do not export to PDF: a PDF is a picture of the report, and you cannot cleanly pull columns out of it. The spreadsheet you save is the raw material for your positive pay file.
Step 3: Find where the check number actually lives
Paychex reports are organized around employees and pay periods, not a tidy "check register," so the check number is not always in an obvious column. The printed number may appear as a check number or voucher number field, and direct deposit rows may show none. Confirm two things before you build the file:
- The check number is the real printed number. The bank matches on the number printed on the physical check. If your export shows a blank, a voucher reference, or an internal sequence, fix it first.
- The number is bare. The bank wants just
1042, notCheck 1042orCHK-1042. Clean the column so it holds only the digits.
Step 4: Filter to checks, and watch the amount column
Remove everything that is not a printed paper check. Delete the direct deposit rows and any summary or subtotal rows, so the file lists one row per physical check. Listing direct deposits as checks makes the bank flag legitimate ones. For the amount, use the net pay, the amount actually printed on the check, not gross pay and not a subtotal. A payroll report can show several dollar columns in one row, so pick the one that equals the check amount. Some bank specs want the amount with no decimal point, so 1042.50 becomes 104250; if yours does, see implied decimal amounts.
Step 5: Check the date format
Your bank's spec expects one specific date format, often MM/DD/YYYY or YYYYMMDD. A date read incorrectly, for example 06/07 versus 07/06, can swap quietly without any error. Use the check date, the issue date of the paycheck, and reformat the column to match your bank's spec.
Step 6: Convert the export with PositivePayMaker
Now reshape the clean export into your bank's exact file layout. Banks each define their own fixed-width or delimited format, and the field positions are account-specific, so typing it by hand is error-prone. PositivePayMaker does the conversion in your browser: upload the Paychex export, map the columns (check number, net pay to amount, check date to issue date), pick your bank's layout, and download a file ready for your bank's portal. It is free and runs entirely client-side, so your payroll data never leaves your browser.
It ships with bank layouts, including specs published by Chase and Huntington, plus a custom format builder. To learn the fields a bank file contains, see the positive pay file format guide, and check supported formats for yours.
Always validate the first file with your bank
Treat the first file as a test. Run it through the file validator to catch structural problems, then send it to your bank and confirm they accept it and the numbers match. A field off by one position can reject the whole batch. If a file comes back rejected, see why positive pay files get rejected. Paychex also publishes a Report Center demonstration. The same workflow applies to other accounting tools.