How to Import Payroll Hours into Paychex Flex (CSV)

Paychex Flex takes hours through a standard payroll import: a CSV of employees and their period hours, matched on the Worker ID that comes from Paychex. It's the same shape as the other big payroll systems, with one Paychex-specific wrinkle worth knowing: import availability and column expectations can vary with how your Flex account was configured, so the first import is worth a five-minute call with your Paychex rep.

01

The file Paychex Flex expects

One row per employee per pay component: Worker ID, pay component, hours, decimals, so regular and overtime arrive on separate rows. Clox exports this from Reports, Export, then Paychex Flex (CSV), using the payroll ID on each profile. If the export isn't in your Reports menu yet, enable the provider first in Settings under Integrations; each enabled provider adds its export format to the menu.

1. 1One-time: confirm with your Paychex rep that payroll imports are enabled on your account and which entry flow they land in as of your configuration; note the answer somewhere the next payroll person will find it.
2. 2Put each worker's Paychex Worker ID into their profile in your tracker.
3. 3Approve the period, export the Paychex Flex CSV.
4. 4In Flex, open the payroll entry flow and import the file where your configuration accepts it.
5. 5Verify totals against your report, resolve unmatched IDs, and submit.

02

The audit habit that pays

Paychex customers skew toward businesses that see workers comp audits, and audits ask for something a totals file can't provide: proof behind the hours. A totals CSV proves nothing by itself. Keep the punch-level record behind every import where you can produce it: who, when, and where each shift started and ended. Clox keeps that record hash-chained, and the workers comp audit guide shows the exact package auditors accept.

03

FAQ

Clox exports the file Paychex expects, backed by punch-level records. Free for 14 days.