If you are a solopreneur or only a few employees and don’t want to subscribe to QuickBooks Payroll add-on services, then you can do the payroll manually. This definitely will take more time in setting up chart of accounts and you have to obtain the CPP, EI, & tax tables from Canada Revenue Agency.
CRA website provides Payroll Deductions Online Calculator where you can calculate the payroll deductions before inputting it into QuickBooks.

In the example below, Jacque Hudspet is an employee in Vancouver, BC with $3,000, - monthly salary, with no other taxable benefits or deductions. CPP is calculated at 4.95% ($3,500 exemption) for both company and employee portion. EI for employee is at 1.88%, while EI for company is 1.4 times EI for employee.

To issue a paycheck:

1. Create Salary/Wages Expense under Payroll Expense. Create CPP-Employee, EI-Employee, & Income Tax-Employee liabilities account under Payroll Liability.

2. From the Main Menu > Banking > Write Cheque.

3. In the Expenses tab > Account, select Salary/Wages Expense and enter gross salary/wages.
4. Move to the next row, select CPP-Employee Liability and enter CPP-Employee amount with minus sign.
5. Move to the next row, select EI-Employee Liability and enter EI-Employee amount with minus sign.
6. Move to the next row, select Income Tax-Employee Liability and enter Income Tax-Employee amount with minus sign.
The cheque amount is the net salary amount.

QB Manual Payroll 1

 

When the monthly payroll tax is due on the 15th of the month after the payday:

1. Create both CPP-Company Expense & EI-Company Expense under Payroll Expense.

2. Open the Write Cheque window again and select Receiver General as payee.

3. In the Expense tab > Account column, select CPP-Company Expense just created and enter the amount.
4. Move to the next row, select EI-Company Expense and enter the amount (1.4x$56.40).
5. Move to the next row, select CPP-Employee Liability and enter the amount you entered when you issued the paycheck without minus sign.
6. Move to the next row, select EI-Employee Liability and enter the amount you entered when you issued the paycheck without minus sign.
7. Move to the next row, select Income Tax-Employee Liability and enter the amount you entered when you issued the paycheck without minus sign.
8. The cheque amount, the total of all the above, is the payroll tax due to government.

 

QB Manual Payroll 2