This integration was built and is supported by Paychex. For ALL setup help and support of this integration, please contact Paychex.

The purpose of this guide is to give you an overview of your Paychex Flex to Deputy integration. The Flex to Deputy connection is a two-way integration in which Flex is the "source of record" for worker information and Deputy collects and transmits payroll data to Flex. Once added to Flex, new or updated worker information should flow to Deputy within 5 minutes to an hour of the change. Payroll data transfers on a schedule set to coincide with the Flex Pay Period Calendar.

How the integration works

If not already completed - your rep will fill out the integration request form for Deputy and work with you to choose the start date for the integration. On the agreed-upon date, a member of the Paychex Integration Support team will take steps to initiate your employee integration. Any new hire saved in Flex will send their data over to Deputy. Your payroll rep may reach out to you to resolve any employee information that cannot be aligned between the two systems.

After starting the Deputy payroll integration, timesheets will be transferred to Flex and then marked as 'Paid' in Deputy. This allows for a one-time import; any adjustments or corrections afterwards must be manually done within Flex.

The integration can be set up to 'delay' when Deputy is checked by 'number of days since Flex pay period End Date' - this can be set up during onboarding and adjusted as needed. This will enable timesheets with disputes to be resolved while still allowing Flex to import the payroll information.

Payroll information is loaded to a worker’s check per-timesheet so any timesheets that are not paid, but are time/pay approved, and not in dispute will post to the worker - any remaining timesheets will be re-tried the next polling cycle from the integration.

Integration data flow chart

Important Items to Note

  • When a new worker is successfully added and saved in Flex, a new worker will be added to the Deputy People roster and populated with the applicable values.

  • When an existing worker in Flex has a change or deletion to one of the mapped data elements, those changes will update the corresponding worker in Deputy.

  • Caution: Any changes made in Deputy to any shared fields will not automatically update in Flex and will be overwritten by the Flex data the next time that worker triggers a sync event.

  • Only the default multiplier rates for 1.5/2.0 for over/double time are supported - on these items, only hours will be sent to Flex which will then handle the factorization calculation on the rates.

  • Shift Codes of "Weekday"/"Saturday"/"Sunday"/"Public holiday" as well as normal hourly "Daily" rate mappings are supported for individual Flex mapping.

  • All other Pay (non-Leave) rates will map to Regular in Flex - A future enhancement for custom rates is pending.

  • The Labor Distribution Product is Required in Flex for labor overrides to be used in Payroll.

Working with Integration Team

Ensure you go over this guide, to get familiar with how the data will be mapped from Flex to Deputy, as the two systems have different names for some of the same data.

Pay special attention to the mapping notes column.

  • Determine when you will be ready to have Flex as the source of record for all new hire information and employee changes.

  • Determine the first payroll you would like to have set-up with the payroll integration.

  • Decide on an email account that you want any error messages to go to.

Paychex® data elements and mapping

Demographic data


Paychex Flex®

Mapping Notes

Last Name

Last Name

Required to create a new record in Deputy

First Name

First Name

Required to create a new record in Deputy



Date of Birth

Birth Date

Start Date

Hire Date

Communications data


Paychex Flex®

Mapping Notes


Personal Email

Mobile Phone

Mobile Phone

Street Address

Street Address 1

Street Address 2

PO Box

Deputy accepts a single line for postal address. The Flex values for Address 1 and Address 2 will be combined for use in this field. PO Box will be used for workers that have one entered.





Postal Code

Postal Code

Compensation/Salary data


Paychex Flex®

Mapping Notes

Hourly Rate

Hourly Rate 1

Deputy offers a variety of predefined templates for pay detail rates. The integration will use the "FLSA Standard" template when creating a new worker.

Please note: Salary information is not mapped between Deputy and Paychex.

Payroll data


Paychex Flex®

Mapping Notes

Area Name / Export Code

Labor Assignment

Defaults to home if unable to find a matching-named Area Name→Labor Assignment. Labor Distribution Product is Required in Flex

Pay / Leave Rules

Earn Code

These will map to Flex Earnings codes.

Payments with a multiplier of 1.5 and 2.0 will be mapped as "Overtime" and "Double Time" respectively

Flex supports multiple Leave Rules of the same type w/ different names and can map them accordingly.

Flex supports Shift Differential codes for "Weekday" / "Saturday" / "Sunday" / "Public holiday" as well as "Daily" named rates.

Any other payrate will be mapped as "Regular" within Flex.

Base Pay Rate

Pay Rate

The pay rate associated with a worker's pay rule & base pay rate will be used to send the appropriate rate over to Flex.

Hours per Timesheet


Location and Organisations

Deputy contains two different ways to represent where an employee works; Business (or Organisation) and Location.

The integration assumes there is exactly one Deputy Business for every Flex ID. A Flex ID may have multiple locations associated with it. The integration checks if the Paychex Location field associated with a new employee matches any location names in Deputy. If so, the worker is added to that location in Deputy. If location name matching is not ideal, you may also choose to set up a default location titled "Paychex Integration New Hires" within Deputy to send new employees to. If no match is found, and the "Paychex Integration New Hires" location is not set up, the worker is added to the first location the Deputy API provides on the location list.

You can distinguish if you're using Business or Location to store different employees by logging into Deputy and checking the following page: You will see each of your businesses listed there, as well as the number of locations in each business:

Businesses within Deputy

Labor Distribution

If you use the Labor Distribution product in Flex you can use the different Areas within Deputy as overrides to assign payment to different assignments within Flex.

  • The Labor Assignment names in Flex must be a unique and one-to-one match to the name used in Deputy.

  • The integration will attempt to match to the Deputy 'Export Code' if available and fall back to the Area Name if not.

  • The 'Export Code' is Deputy's way to let you custom map your Area to a different name without needing to change it internally.

To access this setting, within Deputy:

1. Go to the Locations tab and click Edit Settings, then click on Areas.

2. You can then Add a new Area or Edit an existing Area. Click on the Advanced Area Settings menu.

Edit Area Settings

3. Type in the Export code and click Save.

You can also enter in “SKIP” in this field if you want to bring in the payment, but not override its default assignment in Flex.

Export Code


At times an error can occur with the integration which would require user intervention. Error feedback is provided via email, to the email address you provide during set-up. Only one email can receive errors.

Possible Errors

Potential errors that will be brought to your attention via the email defined during configuration:

  • Incompatible data on an added employee: Max length, special characters in an unexpected place (like Name), missing formats.

  • Information in Deputy could not be updated due to missing information or a systems outage.

Unsupported Actions

  • If a worker's pay rate in Deputy is set to a non-Hourly remuneration (salary), any hourly rate changes in Flex will not flow to Deputy to avoid overwriting the worker's contract details.

  • A worker’s pay rate in Flex changes from Salary to Hourly. The integration cannot change a worker’s pay type in Deputy. If the worker is manually updated in Deputy to an hourly rate, the rate can be maintained in Flex as normal.

See also Exporting to Paychex

This integration was built and is supported by Paychex. For ALL setup help and support of this integration, please contact Paychex.

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