Paychex Flex time tracking for field crews
If you run payroll in Paychex Flex, Friday usually means turning texts and paper timesheets into hours and typing them in by hand. Clox lets your crew clock in from their phones all week, calculates overtime for you, and exports a Paychex Flex import file from one page. This post shows exactly what is in that file and how to set it up once.
JULY 5, 2026 · BY THE CLOX TEAM
You already trust Paychex Flex to run payroll. The part that hurts is everything before it. On Friday you're chasing down who worked which day, adding up hours from texts and paper, splitting out overtime in your head, and then typing all of it into Paychex line by line. Every one of those steps is a chance to key a number wrong, and you find out when someone's check is short.
Clox removes the re-keying. Your crew clocks in from their phones, the hours are totaled by person and job, and Clox writes a file that maps into the Paychex Flex Standard Payroll Import. You review, export, and import. That's the whole loop.
01
How the export works
There are four steps, and only two of them are yours. The crew handles the first one without you.
- Your crew clocks in and out on Clox all week. It's one tap on their phone, it works offline, and you can lock it to a geofenced worksite.
- You review and approve the hours on the web. Hours accumulate by person and project, and overtime is calculated for you.
- You export the Paychex file from the Reports page. Only the payroll systems you selected appear in the export menu.
- You import that file into Paychex Flex using its Standard Payroll Import.
Because the punch is saved on the phone the moment a worker taps, a lost signal at a remote site doesn't lose the time. The punch keeps its real timestamp and syncs when the phone gets signal back.
02
What is in the file
Clox's Paychex export is a CSV built for the Paychex Flex Standard Payroll Import (the preprocessing import). It has 16 columns. Clox writes one row per employee per pay component, so an employee with overtime gets a regular row and an overtime row.
The 16 columns Clox writes for the Paychex Flex Standard Payroll Import.
How overtime is handled. Clox splits overtime before it writes the file. Regular hours go on the regular row and overtime hours go on a separate overtime row, with double-time folded into the overtime hours. You're not doing that math, and you're not splitting it inside Paychex.
Pay Component names have to match
The Pay Component name Clox writes, such as Regular, must exactly match a Pay Item you have configured in Paychex Flex. You set the name in Clox once, in the per-company Paychex settings, so it lines up with your Paychex setup.
03
Set it up once
The setup is a one-time job. After this, every pay period is just review, export, import.
- Go to Settings, then Integrations, then Payroll, and turn on Paychex. From then on Paychex shows up in the Reports export menu.
- Enter your Paychex Client ID and the Pay Component names in the per-company Paychex settings so they match your Paychex Flex Pay Items.
- Give each worker their payroll ID on the Team page. That ID is the Worker ID Clox writes, and it's how Paychex matches the person.
Set every worker's payroll ID
Paychex matches on Worker ID, which is the worker's payroll ID in Clox. If someone is missing their payroll ID, their hours won't match a Paychex employee. Fill these in on the Team page before your first export.
Paychex Flex owns the import screen itself, and their layout changes over time, so follow Paychex's official Flex import documentation for the exact steps to upload a Standard Payroll Import file. Clox's job is to hand you a file that's already formatted for that import. If you would rather map it yourself, the universal Payroll summary CSV always appears in the export menu and drops into any provider.
Try it on your next pay period
You can run one real pay period through Clox before you commit. It's 14 days free, no credit card to start, and a 30-day money-back guarantee. Set up Paychex, let your crew clock in for a week, and export the file to see it for yourself.
You can see what it costs on the pricing page, or start the free trial and set up Paychex today.
04
Common questions
We already do it by hand. Why change?
Doing it by hand works right up until a number is wrong, and then you're fixing a check and re-running part of payroll. The manual steps are the collecting, the adding up, and the typing into Paychex. Clox removes those three. Your crew's taps become the hours, and the hours become a Paychex file. You still review everything before it goes out.
Does it handle overtime?
Yes. Overtime is calculated automatically using standard daily 8-hour and weekly 40-hour defaults, and you can configure those per employee. There's an optional California rule set that adds daily double-time and flags meal breaks for review. Clox splits the overtime out before it writes the file, so the regular and overtime rows are already separated for Paychex.
What if a job runs across two pay periods?
Clox accumulates hours by person and project, and the export is scoped to the pay period you run. The Line Date on every row is the pay-period end date, so hours land in the period they were worked. A job that spans two pay periods simply shows up in both exports, each with its own hours.
What do my workers have to install?
As little as you want. The iPhone app is on the App Store, and anyone can also clock in straight from a phone browser at app.getclox.com without installing anything. You run all the review, approval, and exporting on the web.
Use a different payroll system? Clox also exports to Gusto, ADP, and QuickBooks. See the guides for Gusto, ADP, and QuickBooks.