Run Payroll

This guide will focus mainly on recurring payrolls, but both types of payrolls are mostly similar other than their frequency and purpose. Read more about Off-Cycle payrolls here.

Important considerations before running payroll

  • Ensure bank accounts, tax credits, compensations, and terminations are set up correctly for all employees
  • Ensure benefits and income types are set up correctly for all employees
  • Check that the payroll period’s dates are accurate
  • The typical deadline for running a payroll is 4 business days before the payroll’s pay date, before 4:30pm EST

Every payroll run is divided into three steps: Edit, Review, and lastly Complete & Pay.

Edit Payroll

  • Search, Sort and Filter employees
  • Regular pay for salaried employees
  • Regular pay for hourly employees
  • Add extra pay
  • Add reimbursement
  • Confirm payment method
  • Finish editing

Search, Sort and Filter employees

Depending on the number of employees on payroll, you may find yourself constantly navigating between pages and profiles in order to ensure all your inputs are set correctly and payments are accurate. In order to help bring organization to the payroll run screen, we built the ability to search, sort and filter information to help ensure payroll gets processed on time and exactly as planned.


Whether you need to make an adjustment, add an expense or double-check a payment, simply enter in the employees name in the search box to pull up all their payment types - no more continuous scrolling to find the employee you're looking for.


Need to reorder the employees shown on the payroll run screen? Simply click on the arrow above the employee name column to sort by A-Z first name or last.


You can now build powerful, multi-level filters to find the exact group of employees you're looking for. Wether, you want to view all terminated employees, all employees being given a bonus and reimbursement or even by department, just click on the drop-down, hover over the criteria and select the filter group.

You can then narrow your filter even further by clicking into the drop-down again and selecting another filter group. This will tell payroll to only show employees that fit within both criteria. You can continue adding on filter levels to further narrow down you're search

You can currently filter by:

  • Office Location - Employee's belonging to any of your company's offices
  • Department - any department at your company
  • Compensation Type - Employees paid by cheque or direct deposit
  • Additional Income - Income types set up in your company's payroll
  • Payments - Regular payments that are automatically prorated for new hires, compensation changes or terminated employees or filter by reimbursement payments
  • Status - New hires, Rehires or Terminated during a given pay period
  • Reimbursement - expense reimbursements paid out during the period
  • Wage Type - Hourly or salaried employees

Regular pay for salaried employees

Within each payroll, every employee’s salary earning for the period is pre-calculated based on the annual salary divided by the number of periods. These amounts can be edited if necessary to accommodate for special circumstances.


Any employee who receive a compensation change during the payroll cycle will also have their prorated salary calculated automatically.

Regular pay for hourly employees

Employees that are paid based on hours worked require the amount of hours to be entered each payroll. There are two ways to enter hours for your hourly employees: entered manually, or uploaded through a template.

Manual method

For each applicable employee, enter the hours worked in the box denoted by “H”, which stands for “hourly”. The hourly rate is prefilled based on the compensation that is set up in the employee’s profile.

Upload method

Click Download Hours Template in top right corner to download a spreadsheet template for entering employee hours in bulk

  1. Fill in template and save. Only regular and overtime hours can be entered.
  2. Select Upload hours in the top right corner, select file.
  3. Click Next.
  4. Vacation pay will automatically calculate based on hours entered as well as the percentage set up on employee profile

To record and pay for overtime work, select +Overtime. A new input field will be displayed with 1.5x the regular hourly rate. Here you can enter the number of overtime hours worked.

Add Extra Pay

Aside from paying your employees their regular earnings you can pay additional income as well. Learn more about income types here.

The income type options available under Extra Pay are:

To add extra pay, select the applicable income type and enter the amount for the period. Once created, the employee’s gross pay will increase to reflect the extra pay amount, as well as applicable vacation pay.

Add Reimbursement

This is a non-taxable amount and is usually how expenses are reimbursed. Gross pay will not increase if an amount is entered here, and reimbursement will show up as a separate line item on the employee’s paystub.

Confirm payment method

Employees who had their bank account correctly set up will have their payment method set to direct deposit by default. Each employee can also be individually marked as pay by cheque if necessary. The total amounts paid by cheque will be kept as records, but the payments are not processed through Humi Payroll.

Finish editing

Once the payroll is ready to be reviewed, click Next on the bottom right to finish editing. This is the stage where Humi Payroll will calculate deduction amounts such as CPP, EI, and income tax. All amounts within the payroll will also become temporarily locked-in to prevent changes in employees’ compensations or benefits, or other admin’s conflicting edits from affecting the current payroll.

Alternatively you can also click on Edit on the bottom left to return to the Edit page.

Review Payroll

  • Review payroll summary
  • Finish reviewing

Review payroll summary

The payroll’s summary is broken down into three main sections, with an additional EHT section if the payroll is run within provinces that have requirements for employer payroll tax such as Employer Health Tax.

Payroll Obligation

A payroll’s obligation can generally be seen as Total employee net pay + CRA Remittance + Other deductions. In this section, it is important to review Account Debit as this is the amount that will be taken from your bank account when the payroll is completed and its payments processed.

Important note on payroll deadlines:

If a payroll is run after its deadline, the payment method for all employees will be automatically changed to cheque and the company should issue the payments in cheque. This is to prevent employees from being paid later than intended. Note that the deduction amounts as well as reimbursements will still be debited and processed through Humi Payroll.

However, if the payroll is run after its remittance due date, Humi Payroll will not debit or remit any payroll obligations. Payroll administrators are encouraged to remit directly to the CRA.

For more information on late payments please reach out to

Employee Net Pay

This section displays the total amounts that are paid by direct deposit and by cheque. Payroll administrators can use these amounts to determine whether manual actions are needed.

Cheque - Amount that should be paid manually by cheque to employees

Direct Deposit - Amount that is automatically processed through Humi Payroll

CRA Remittance

This section provides a breakdown of the statutory payroll deductions that will be remitted to CRA on your behalf based on your remittance schedule. It is highly recommended that you verify all numbers shown are accurate, as under-remittances may result in penalties and interests imposed by the CRA.

Employer Payroll Tax

Depending on the province the employees are paid in, the payroll may contain information on employer payroll tax obligations such as Employer Health Tax amounts for employers that pay their employees in Ontario. Humi Payroll does not remit this amount but does provide a report of the calculation, amount due and due date. Click on the detail button to see an in-depth breakdown of the amounts.

  • The calculated Employer Payroll Tax amounts are estimations only, as each employer may have already remitted payroll taxes in the past or has applicable carried-over tax credits.

Finish reviewing

Once the payroll information are entered and the payroll summary reviewed, it is highly recommended that payroll administrators export a Payroll Register report for the period to confirm that all line items are calculated accurately. Learn more about Payroll Register report here.

If you are certain all records are set up accurately, click Complete & Pay on the bottom right.

Complete and Pay

This is the stage where all records within the payroll become final and permanently locked-in. Humi Payroll will then process payments to employees and remittances to the CRA based on the records from this payroll.

Payments are processed in batches through the Canadian banking network. Employees generally receive pay the morning of pay day at roughly 6:00am EST.

Information from this payroll will also become part of your employees’ record for the tax year which will be reported on T4. You can now view this payroll in the payroll records section.

At this stage If errors are discovered within the payroll it is highly recommended that you reach out to immediately.