Conducting payroll can be one of organizations' most tedious and time-consuming processes. 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. This article will walk you through the key steps to streamline your payroll with Paychex Flex.

This article will be broken down into the following sections:

Before getting started with the set up, it's a good idea to review certain aspects of the integration to make sure it's relevant to you.

Paychex charges a flat monthly fee of $15 USD for each connected client ID for this payroll integration. At present, Connecteam covers this integration cost for you, the coverage is provided automatically, with no reimbursement required. However, please note that these terms may be subject to change in the future. Should there be any changes, you will be notified in advance. If a fee is introduced, you will have the option to disconnect the integration at any time to avoid incurring charges.

The integration supports both W-2 employees and 1099 independent contractors. In Connecteam's UI, both types appear together in the same user list, and they are matched to their Paychex workers in the same way. The distinction between W-2 and 1099 is handled on the Paychex side. Contractors are paid using 1099 earning components in Paychex (for example, 1099 Earnings or 1099 MISC Other Income), under the 1099-MISC classification.
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Salaried employees who are not eligible for overtime can be included in the export. This is currently in beta. To turn it on for your account, contact our support team.

For each of these employees, Connecteam sends:

For example, an employee with 40 standard hours who took 8 hours of PTO is sent with 32 memo hours and 8 PTO hours.

Salaried employees do not need to track time in Connecteam. Their hours come from the Standard hours field on their Employment tab, not from their timesheet. If a salaried employee does clock in and out, those punches are not used and do not change what is sent to Paychex. Paid time off is the only thing we take from their timesheet.

Memo hours and time off hours appear on the paycheck for reference only. They do not change what the employee is paid. The salary amount does.

Note: Salaried employees who are eligible for overtime are not supported yet.
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While setting up the integration, in the step where you match your pay rules, you can choose whether to send your Connecteam pay rates along with the hours:

When you choose to include pay rates:

Note: This option is only available if pay rates are enabled in your Connecteam account. If they are not, the hours are exported without rates.
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If you chose not to include your Connecteam pay rates in the export, Paychex determines which rate to apply in the following order:

If you want a worker to be paid based on their standard worker rate, make sure to remove any rate stored on their Home Labor Assignment and Home Job in Paychex, so that Paychex falls back to the worker rate.
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Before getting started the following things need to be set up to connect the integration.

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

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

The steps are the following:

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!

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`

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 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.

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`.

Both W-2 employees and 1099 independent contractors appear together in this list, and both are matched to their Paychex workers in the same way.

At the top of this step you choose whether to include your Connecteam pay rates in the export:

See Sending Your Connecteam Pay Rates to Paychex for the full details of what each option does. This option is only available if pay rates are enabled in your Connecteam account.

Below that, you need to match your pay rules in Connecteam and the pay items in Paychex. There are two options:

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`.

If you have matched salaried employees, you will also be asked to choose which Paychex pay component to use for their salary.

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.

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.

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.

Note: Any recurring earnings configured for a worker in Paychex are automatically added to their pay entry. These appear as earning lines without hours and are not payable on their own. If you don't need a recurring earning for a given payroll, remove it from the worker's pay entry in Paychex.

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'.

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'.

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.
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Make sure to follow the setup steps, especially when matching the pay rules for regular hours. If the matching for regular hours is not set properly, you won't be able to see the hours on Paychex.
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You need to read carefully the error message provided. For example, if you receive the message: "You have entered hours/units but there is no default rate available for this pay component..." - it means you should define a default rate for this pay component on your Paychex account. This can also happen when you export hours without pay rates for a worker who has no default rate in Paychex. Either add the default rate in Paychex, or choose to include your Connecteam pay rates in the export.

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.
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You need to approve the integration with Connecteam. Head over to Company settings -> Integrated apps -> under Connecteam integration approve the integration
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The hours you export from Connecteam will always overwrite your hours in Paychex.
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This likely means that you have made changes to your Connecteam account since setting up the integration with Paychex. You may have added new users, jobs / sub-jobs, or PTO policies. You will need to match these items before exporting the data to Paychex. To do this, simply click on the `Resolve now` button, match the items, and click, `Continue`.
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That's OK! When matching your users you have the option not to include the user in the integration.
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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.
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​Please make sure that the workers on Paychex are marked as active. Both W-2 employees and 1099 independent contractors are now supported, so both worker types will appear in the list and can be imported and matched in the same way.
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1099 independent contractors are now supported. They appear together with your W-2 employees in the same user list and are matched to their Paychex workers in the same way. Please make sure the contractor is marked as active in Paychex.
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Yes. In the step where you match your pay rules, choose Include pay rates. Every line of hours is then sent with the rate it was earned at in Connecteam, and that rate is used on the paycheck instead of the rate stored in Paychex. If you choose Don't include pay rates, only hours are sent and Paychex prices them with its own rates. The option is only available if pay rates are enabled in your Connecteam account.
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Paychex does the multiplication. In line with Paychex's guidelines, we send the employee's base hourly rate on the overtime line, and during the payroll process Paychex calculates the final amount using the multiplier configured on the pay component you matched your overtime to. Make sure those components are set up with the right factor, for example 1.5 for overtime and 2 for double overtime. Keeping the multiplier in Paychex also means that any hours a payroll admin adds to the check later are priced the same way as the hours we sent.
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The pay component your overtime is matched to has no multiplier configured in Paychex. Since Connecteam sends the base rate, the component has to apply the factor. Open the pay component in Paychex, set the correct multiplier, and export again. If you are not sure how to configure it, your Paychex representative can help.
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When you include pay rates, hours are grouped by the rate they were earned at. If an employee worked the same pay item at two different rates during the period, for example because of a job specific rate or a rate change mid period, each rate appears on its own line. Without pay rates, those hours are combined into a single line.
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If you chose not to include your Connecteam pay rates, Paychex applies rates in this order: the worker's Home Labor Assignment rate, then their Home Job rate, then their standard worker rate. If a rate is stored on the Home Labor Assignment or Home Job, it will be used instead of the standard worker rate. To have the worker paid based on their standard rate, remove the rate stored on their Home Labor Assignment and Home Job in Paychex, or choose to include your Connecteam pay rates in the export.
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These are most likely recurring earnings configured for the worker in Paychex, which are automatically added to the pay entry. Earning lines without hours will appear but are not payable on their own. If you don't need a recurring earning for a given payroll, remove it from the worker's pay entry in Paychex.
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Yes, for salaried employees who are not eligible for overtime. This is currently in beta, so contact our support team to turn it on for your account. Connecteam sends their salary amount from Paychex together with memo hours based on their standard hours in Connecteam. Salaried employees who are eligible for overtime are not supported yet.
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Open the employee's profile and go to the Employment tab. Under compensation details, set Pay type to Salaried and Overtime eligibility to Not eligible, and fill in their Standard hours. In the integration setup, choose which Paychex pay component to use for salary.
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No. Their hours come from the Standard hours field on their Employment tab, not from their timesheet. If they do clock in and out in Connecteam, those punches are not used and do not change what is sent to Paychex. The only thing we take from their timesheet is their paid time off.
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We take the standard hours from the employee's Employment tab and subtract any paid time off they took during the pay period. Their tracked hours are not part of the calculation. For example, an employee with 40 standard hours who took 8 hours of PTO is sent with 32 memo hours and 8 PTO hours, whether or not they clocked in that week. If standard hours is empty, we send 0 memo hours and the salary amount is still sent.
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From the employee's compensation in Paychex, as of the check date of the pay period you are exporting. If the salary is stored as an annual amount, we divide it by the number of pay periods in your pay calendar for that year. If a raise takes effect by the check date, the new amount is used.
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No. The include pay rates option only affects hourly employees. Salaried employees are always exported with their salary amount, and their memo hours and time off are sent without rates.
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The export stops and the error names the employee. Add the salary amount to that employee's compensation in Paychex and export again. Nothing is sent until every salary is read successfully, so your existing pay entries in Paychex stay as they were.
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Only if you use the Paychex Payroll Time Off Accrual service and the time off policy is mapped. In that case the hours are deducted from the balance when you process payroll. Without that service you manage balances yourself, the same as for hourly employees.
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Yes. Their hours come from the Standard hours field rather than from the timesheet, so they are exported with their salary and their standard hours regardless of whether they tracked any time.
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Their salary is prorated based on the employment start date on their Employment tab in Connecteam, according to the number of calendar days they were employed within the period. If their start date is after the pay period ends, they are not included in that export.
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Create a separate time clock for each pay cycle and connect each one to Paychex. The pay cycle in your Time Clock payroll settings determines the pay period we export, and the salary amount we send is based on that period.
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