Payroll, benefits, HR and more.
- Payroll
- Benefits
- Team Management
- Accounting & Integrations
- Employees & Contractors
- Account Setup & Maintenance
- State Registration & Compliance

Integrate with Aplos
You can sync payroll info from Gusto to your Aplos Accounting account. To set this up:
- Navigate to the Accounting section of your Aplos account.
- Click Payroll.
- Click Log in to your Gusto account.
- Enter your Gusto login credentials.
- Click Authorize.
- Click Go To Setup to set up how the payroll details will map to your Aplos accounts.
- 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.
- Click Save.
- You will now see the active integration in your Settings tab of your Gusto account.
Account mappings
Edit your global account mappings
- Navigate to the Payruns for Import page in Aplos.
- Click the gear icon in the top right hand corner.
Customize your account mappings by employee
- After you’ve clicked import for a payrun, uncheck the box in the Edit Mapping column.
- 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 applied on future payroll imports until otherwise edited.
- Click Save.
- The total accounts customized will appear in the Custom Mappings column.
Remove or reactivate a Payrun
- Click Show History.
- Click Reactivate if you’d like to make a previously dismissed payroll available for import.
- 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.
Questions and Answers
Q: Does information sync over by employee?
A: Yes. Everything from payroll taxes, wages, and reimbursements can be mapped on an individual level. Click 'Account mappings' above to learn more.
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.
- Please remember to ensure the allowance is an official housing allowance that is excluded from taxable gross wages.
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 enter the yearly totals in Gusto when confirming your 2020 tax information.
Q: Does the sync work on regular, off-cycle, and bonus payrolls?
A: Yes.
Q: Will I be able to distinguish between a direct deposit or check payment to an employee in Aplos?
A: Yes.
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.
Payroll, benefits, HR and more.