Integrate with Aplos

Aplos is a software solution for churches and nonprofits. It allows you to manage your books, donors, and members all in one place. Services include:

  • Nonprofit and church accounting
  • Donor management
  • Member management
  • E-filing of IRS returns (990-N, 990-EZ)

Gusto connects to Aplos Accounting to automatically track your payroll and tax payments. We also support the W-2 requirements and unique church payroll needs for pastor housing allowances and tax exemptions.

Click on the headers below to learn more or visit Aplos' help center for additional information.

Integration setup

  1. Navigate to the Accounting section of your Aplos account.
  2. Click Payroll.
  3. Click Log in to your Gusto account.
  4. Enter your Gusto login credentials.
  5. Click Authorize.
  6. Click Go To Setup to set up how the payroll details will map to your Aplos accounts.
  7. Select the Fund account and assign an expense or liability account for each category.
    • Click the + next to a category and adjust the percentages to split the entry between multiple accounts.
    • Your bank account election can be an expense or an asset account.
  8. Click Save.

You will now see the active integration in your Settings tab of your Gusto account. 

Sync your payroll

Once your accounts have been mapped you can sync your payrolls from Gusto to Aplos.

  1. Navigate to your Available Payruns for Import page in your Aplos account.
    • Pay period, company debit amount, and number of employees will appear for each payroll run.
  2. Click Import to sync the desired payroll(s).
    • Employee ID, name, gross pay, and net pay will appear for review.
    • The global account mappings selected during the integration setup will automatically be applied unless edited.
  3. Click Next.
  4. Review the journal entry that will be created.
  5. Click Import or Import & Exit Payroll
    • Import: Imports and returns you to the list of payruns.
    • Import & Exit Payroll: Imports and takes you to the journal entry created.

Payrolls you do not want to sync can be dismissed using the same method.

Account mappings

Edit your global account mappings:

  1. Navigate to the Payruns for Import page in Aplos.
  2. Click the gear icon in the top right hand corner.

Customize your account mappings by employee:

  1. After you’ve clicked import for a payrun, uncheck the box in the Edit Mapping column.
  2. To override the global mapping setting(s) and customize to the employee, select a new account in the field you’d like to override and enter a percentage.
    • Fields not edited will apply the global settings when mapping accounts.
    • Employee’s custom mappings will be apply on future payroll imports until otherwise edited.
  3. Click Save.
    • The total accounts customized will appear in the Custom Mappings column.

Remove or reactivate a payrun

  1. Click Show History.
  2. Click Reactivate if you’d like to make a previously dismissed payroll available for import.
  3. Click Remove Payrun if you want to remove any existence of that previously imported payrun in Aplos.
    • The payrun will then become available to import or dismiss again.


Q: How do I set up a tax exemption?

A: There are two types of exemptions, employee or employer:

Q: How do I add a reimbursable housing allowance when processing payroll?

A: Follow these instructions to add the housing allowance amount as a reimbursement.

Q: How do I handle the annual housing allowance so it is reported on Form W-2?

A: You can reimburse your pastors throughout the year, then at year end be sure to contact us with the total amount you'd like to report in Box 14 on Form W-2.

Q: Do you have any additional resources we can reference?

A: Check out this IRS resource with tax information, filing requirements, and exemption information for charities and other non-profits.


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