FAQs: Payroll processing

This article includes answers and troubleshooting tips and tricks for some of the most common payroll processing questions, including:

• late processing
• missed payrolls

I missed my payroll processing deadline. What are my options?

If you've missed your payroll processing deadline and your payroll is late, you have two options:

1. change your pay date to accommodate your processing timeline
2. run a manual payroll

Changing your pay date will mean that your employees are not paid on their typical schedule, but Wagepoint will take care of money movement as usual. Conversely, running a manual payroll will maintain your pay date, but you'll need to take care of money movement outside of Wagepoint. 

The table below summarizes the pros and cons of each option. 

	Option 1: Change pay date	Option 2: Run manual payroll
Money movement	Wagepoint, via direct deposit	Manual, via cheque or e-transfer
Impact on pay date	Delay pay date	Maintain pay date
Impact on reports	None.	None.
Impact on remittances (CRA taxes, employer taxes, and Workers' Compensation)	None.	You must remit the relevant taxes yourself, outside of Wagepoint. However, you can still utilize Reports to collect the needed information.

Once you have selected the best method for you, follow the appropriate instructions below.

• Option 1: Change pay date

  1. Begin the Run payroll workflow as usual.

  2. Under Pay date, select a new pay date. The system may automatically recommend the next available pay date based on your processing timeline.

  

  3. Ensure the checkboxes next to Direct deposit and Remit taxes are checked if you would like to use these features.

  4. Click Continue and proceed through the Run payroll workflow as usual.

• Option 2: Run a manual payroll

  This options involves turning off direct deposit and remittances, so Wagepoint will not complete any money movement on your behalf. Instead, you must pay your employees manually via cheque or e-transfer and remit any employer taxes yourself.

  Note: Wagepoint cannot issue cheques or transfers on your behalf.

  Part one: Turn off direct deposit and remittances

  1. In the navigation bar, go to Settings.

  2. Under Payroll settings, select General settings.

  3. Uncheck the boxes next to Remit Workers' Compensation, Remit source deductions, and Pay by direct deposit. An effective date will appear next to each setting.

  Note: You can also turn off direct deposit within the payroll workflow.
  
  4. (If applicable) If you have remittances for ON EHT set up, you will also need to turn this setting off. Navigate to Settings > Employer taxes, and select the Ontario tab. Click Edit, then uncheck the box next to Remit EHT. An effective date will appear. Click Save.
  
  

  Part two: Run a manual payroll

  1. Begin the Run payroll workflow as usual.

  2. On Step 1, select your Pay date and ensure that the boxes next to Direct deposit and Remit taxes are turned off. You may need to uncheck the boxes before you can select the desired pay date.

  

  3. Complete the Run payroll workflow.

  Reminder: You must pay your employees via cheque or e-transfer, and submit your remittances yourself outside of Wagepoint. You can use the Payroll taxes report and Workers' Compensation report to find the relevant reporting details.

  You may also wish to turn these settings back on after your manual payroll has been processed.

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I thought I ran payroll, but nothing came through in my bank account. What went wrong?

This situation most often occurs when direct deposit was turned off for the payroll. To check if your payroll was run without direct deposit:

1. In the navigation bar, go to Reports > Deposit summary.

2. Locate the Cheque payment section. If employees are listed here, then direct deposit was turned off and the employees should be paid by cheque.

If this was unintentional, your next step is to ensure that you have direct deposit and/or remit source deductions enabled for your pay runs. Follow these steps:

1. In the top navigation bar, click your company name and select Company settings from the drop-down menu.

2. On the General settings page, review your payroll settings and make any changes. 

If you would like to pay your employees using direct deposit and have Wagepoint remit source deductions and Workers' Compensation on your behalf, then you'll keep these settings turned on most of the time.

However, there are some situations where you may prefer to have these settings turned off, such as:

• direct deposit
  • you are running an extra payroll and you need to pay an employee immediately, there would be no time to process the bank transaction. With direct deposit turned off, you can pay them via cheque or e-transfer immediately rather than waiting 3 business days for a direct deposit.
  • you simply prefer to pay your employees directly, on the day you process payroll for your reporting purposes.
  • you missed your payroll deadline and would like to run a manual payroll instead.
• source deductions
  • you are a Quarterly Remitter who does not wish to send source deductions monthly.
  • you have a separate accounting program you use to remit your source deductions and keep your bookkeeping in order.

You may also find these additional articles useful:

• Set up direct deposits
• Set up and manage employer taxes

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How can I double-check that my payroll is processed as expected?

You can review your recently approved and processed payrolls to ensure that they have processed as you expected, or you can check whether your payroll was submitted with direct deposit and remittances on the Invoices report.

Review Approved or Finalized payrolls:

1. In the navigation bar, go to Payroll.

2. Select the appropriate tab:

• the Approved tab will show any recently approved payrolls
• the Finalized tab will show all payrolls that you have processed on your account

Review the Invoices report:

1. In the navigation bar, go to Reports.

2. Select the Invoices report.

3. In the report filters, ensure that the correct pay period is selected.

4. Under Type, review the available report types:

• If a Net pay type is generated, then the payroll had direct deposit turned on.
• If a Tax remittance type is available, then your remittances were also collected by Wagepoint.

If this is empty, you will need to manually send your remittance to the CRA directly. You can find the total you'll need to send by using the Payroll taxes report.

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When I run payroll, no federal or provincial taxes are deducted. What's happening?

Ensure you've selected the appropriate tax claim code for the employee. Depending on the claim code selected, the pay may not have been substantial enough to require these deductions. You can check using the CRA Payroll deductions calculator. If you still believe there is a calculator error, reach out to [e-mail] and we can troubleshoot with you.