How to Integrate with Paychex Flex

Your step-by-step guide to integrating with Paychex

Shoshana Fleischmann avatar
Written by Shoshana Fleischmann
Updated over a week ago

Conducting payroll can be one of the most tedious and time-consuming processes for organizations. At Connecteam, we have made it our mission to simplify that process and make it as quick and easy as possible so that you can focus your efforts on what matters the most. In this article, we will walk you through the key steps to streamline your payroll with Paychex Flex.

Additional Integration Fee

Paychex bills a flat monthly fee of 15 USD for each connected client ID. Connecteam generously covers your first month of integration, then you’ll be charged with a separate monthly invoice from Paychex. The charge applies from the month following the integration, with no proration for partial months. You can disconnect anytime to cancel.

Before we get started, here is a quick summary of what can be transferred:

  • Regular hours

  • Overtime hours

  • Double overtime hours

  • PTO

This article is broken down into the following sections:

Things to Do Before Integrating Connecteam and Paychex

In Connecteam:

In Paychex:

  • Set up the workers

  • If needed, set up the labor assignments

  • If needed, set up the overtime and time off earnings

  • Set payroll cycle periods

💡Tip: We highly recommend following Paychex's guide on payroll setup before exporting from Connecteam.

Setting Up The Paychex Integration

Once you have done these we can begin with the steps to connect the integration.

The steps are the following:

  1. Ensure the payroll period matches in Connecteam and Paychex

  2. Set up the connection between Paychex & Connecteam

  3. Match Connecteam users with Paychex workers

  4. Match Connecteam pay rules with Paychex pay items

  5. Match Connecteam jobs (and sub-jobs) with Paychex labor assignments

  6. Export timesheets to Paychex

Before beginning the set up please make sure that your employees' names are identical between Connecteam and Paychex as that will speed up the matching process. If they are not the same you will get the option to manually match the employees in Connecteam.

Now, let's set up the integration!

Step 1: Ensure the Payroll Period Matches in Connecteam and Paychex

In Connecteam: Go to your Time Clock settings and enter the payroll tab.

In Paychex: Go to Payroll Center, click on `More Options`, and select `Add New Pay Period`

Step 2: Set Up the Connection Between Paychex & Connecteam

To begin, click on the settings tab on the time clock, scroll down, and click on integrations on the sidebar. From here you can navigate to Paychex click on Connect, and then Connect to Paychex.

Enter your Paychex company ID in order to move to the next step.

You can find it below your company name in the Paychex Flex platform:

Then you will be redirected to Paychex to approve the connection on their side.

Once the connection has been made successfully you’ll need to click on `Continue to setup` to begin setting up the integration.

Step 3: Match Connecteam Users With Paychex Workers

From here you will begin matching any users that were not automatically matched by name. If all users are matched, you can press continue to move forward. If for whatever reason a user was auto-matched incorrectly, this can be changed manually. If you don't want a user to be included in the integration you can mark the `Don't include worker in integration`.

Step 4: Match Connecteam Pay Rules with Paychex Pay Items

Here you need to match your pay rules in Connecteam and the pay items in Paychex.

If you created at least one overtime rule with a 1.5x multiplier, an `Overtime` Connecteam pay rule will be automatically added to the integration, and can be matched to the pay item in Paychex. In case you have multiple 1.5x overtime rules, all the hours under these rules will be aggregated into this `Overtime` pay rule.

If you created at least one double overtime rule with a 2x multiplier, a `Double overtime` Connecteam pay rule will be automatically added to the integration, and can be matched to the pay item in Paychex. In case you have multiple 2x overtime rules, all the hours under these rules will be aggregated into this `Double overtime` pay rule.

Below the working hours pay rules, you’ll find all your Connecteam paid time off pay rules that can be matched to their pay items in Paychex.

If there is a pay rule you do not want to include you can select the option `Don’t include rule`.

Step 5: Match Connecteam jobs (and sub-jobs) with Paychex labor assignments

Here you can select whether you would like to exclude Connecteam jobs from your export, or to include them and then split the working hours based on them.

If you decide to include the jobs, the next step would be to assign them to their matched Paychex labor assignments.

If you use sub-jobs, you can include them in the integration by matching them to the labor assignments in Paychex.

Once you complete the steps above, click on 'Complete setup'.

After closing the setup confirmation modal, make sure to click on `Save changes` in the Integrations setting page to save all the changes.

Now it's time for the final step, actually exporting your payroll to Paychex.

Step 6: Export Timesheets to Paychex

Head to your time clock, to the timesheets tab, click on `Export`, then click on `Export to Paychex`. The export is based on the selected date range and selected employees in the timesheet. Employees can be filtered out if needed.

Next Steps in Paychex

Great, now that you have successfully exported to Paychex you will need to check that the hour units for every pay item have synced to your workers in Paychex.

To do so, click on Payroll Center. Then select the required Check Date and click on 'Resume'. Go over each employee check, review the hours exported, and make manual adjustments if needed.

Once you are satisfied that the timesheet data has been exported correctly, click on 'Review & Submit' to move to the next step on Paychex.

How to Update the Setup Integration After You Added New Items

As your company grows and changes you will likely add new items, these could be new users, jobs / sub-jobs, or time off policies. Before these items can be exported to Paychex they need to be matched. To do this enter the time clock, click on 'Export', find the 'Export to Paychex' option, and click on the settings icon. Match the new items and press 'Complete setup'.

How to Disconnect the Paychex Integration

If for whatever reason you need to disconnect the integration you can do so by heading to the Time Clock clicking on settings, entering the integrations tab, and clicking on 'Disconnect'.

Frequently Asked Questions

Can I connect more than one Time Clock to my Paychex company?

Yes, every time clock in Connecteam can be connected to the same company ID in Paychex. Note that you will need to set up the integration in the settings for each time clock.

Can I connect multiple Paychex companies to a one-time clock?

No, a time clock can only be connected to one Paychex company. This prevents you from accidentally running the same payroll in two places and potentially overpaying your employees.

What happens if I export the same payroll period twice?

The hours you export from Connecteam will always overwrite your hours in Paychex.

When I click on Export to Paychex I receive an error from Connecteam telling me that I have unmatched items. What does it mean and what should I do?

This likely means that you have made changes to your Connecteam account since setting up the integration with Paychex. It’s possible that you have added new users, jobs / sub-jobs, or PTO policies. You will need to match these items prior to exporting the data to Paychex. To do this, simply click on the `Resolve now` button, match the items, and click, `Continue`.

Some of my Connecteam users should not be matched to Paychex. What should I should do?

That's OK! When matching your users you have the option not to include the user in the integration.

I am struggling with connecting my Paychex integration, what can I do?

If you have issues with connecting your Paychex integration, you can always reach out to us on our Live Chat, or email us at [email protected] and we will be happy to assist! You can also request a phone call through both channels, and our team will help you further.

Need more guidance? 🙋 Our LIVE support team (at the bottom right corner of your screen) replies to ANY question.

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