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QuickBooks Online Advanced Payroll - Getting started

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Welcome to QuickBooks Online Advanced Payroll

Note: There is a change to your Advanced Payroll Experience. Click here to learn about the change and it's timing.

Using standard QuickBooks Online Payroll? See Turn on and set up payroll.

Follow this guide to complete your payroll setup quickly and accurately

Required documents

Having the below information handy will make the setup process easier:

  1. Your payroll registration notice from the Canada Revenue Agency (CRA) which has important company information like your legal name, business address and CRA payroll account number. You'll also need the letter from the CRA indicating your remittance frequency
  2. A cheque from your business bank account or another document that contains all the banking details required to complete your bank setup
  3. Any documents you’ve received from provincial tax agencies or labour boards, such as your Workers' compensation account details or applicable provincial taxes, like the Employer Health Tax in Ontario
  4. Your employees’ federal and provincial TD1 forms with all relevant personal details such as full name, birth date, and Social Insurance Number (SIN) completed
  5. A copy of voided cheques from each of your employees or contractors to set up direct deposit

If you're switching payroll providers, you should also generate a report of all employee wages and taxes paid, as well as the amounts for any employer taxes. This information will need to be entered into QuickBooks Online Advanced Payroll as a part of the year-end reporting requirements.

Sign up for QuickBooks Online Advanced Payroll

  1. Open your QuickBooks Online account.
  2. Select Employees or Payroll menu.
  3. Select Set up Payroll.
  4. Select the features that matter to you to see a product comparison of our two payroll offerings.
  5. Use the price calculator to the left of the feature chart to verify your potential cost for QuickBooks Online Advanced Payroll.
  6. Select Free 30 day trial under the Advanced Payroll powered by Wagepoint column.
  7. Select Agree & connect.

Set up

  • Once you've signed up, you'll see a Set up payroll screen with five sections to fill out.
  • Select Add to enter the information in each section.
  • You can also Edit a section prior to submitting the information. See below for details on what information is required for each section.

Advanced Payroll Set up Screen

Enter your company information

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Tell us a bit about your company. We'll use this information on your payroll tax forms.

  1. Legal company name (The business name you use on government forms and legal documents),
  2. Company address, Email (We'll send you payroll reminders and notifications)
  3. Phone number (used for tax forms)
  4. You can also enter in a Promo Code if one was provided.
  5. When completed, select Done.

Enter your payroll tax details

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We take care of all tax payments to the government on your behalf. If you would like to be responsible for making those payments yourself, you can turn off this feature. Quarterly remittances are not supported at this time. If you are are unsure, please contact the CRA for more information.

CRA Account number

  • Payroll account number: Your 9-digit business number + RP + your 4-digit account number. (like this: 123456789 RP0001)
    • You'll use your payroll account number to identify yourself to the CRA on payroll forms or when you remit taxes.
  • Quebec payroll account number: Your 10-digit Québec Enterprise Number (NEQ) + RS + your 4-digit account number. (like this: 1234567890 RS0001)
    • You'll use your Québec payroll number to identify yourself to Revenu Québec on payroll forms or when you remit payroll taxes.

Note: Please ensure these numbers are accurate to avoid missed payments.

Remittance frequency

Your remittance frequency tells us how often you send the payroll taxes to the CRA or Revenu Québec. This includes the taxes you pay and the taxes you withhold from employees' pay cheques. If the CRA or Revenu Québec hasn't told you how often to remit your taxes, select monthly. They'll let you know if you need to start remitting more often, and you can change your frequency in your payroll settings at any time.

Frequency Due Date
Monthly (Non-accelerated)
  • 15th of the following month
Bi-weekly (Accelerated threshold 1)
  • 25th of the month for remuneration that you pay or give from the 1st to the 15th of the month inclusive
  • 10th of the next month for remuneration that you pay or give from the 16th to the last day of the month
Weekly (Accelerated threshold 2) Due on the 3rd working day after the end of the following:
  • From the 1st to the 7th day of the month, inclusive
  • From the 8th to the 14th day of the month, inclusive
  • From the 15th to the 21st day of the month, inclusive
  • From the 22nd to the last day of the month, inclusive

Note: If you opt in for this feature, the taxes will be withdrawn from the bank account on file when you run payroll, and held in trust & remitted on your behalf according to the remittance frequency you chose during the set up. For more information on remittance frequencies, please visit QuickBooks Online Advanced Payroll automatically sets the pay period and pay dates after your first payroll in the system.

Workers' compensation

It covers lost wages, healthcare and rehabilitation services for workers who are injured on the job, and protects you from lawsuits from injured workers. If you hire employees or contractors, you probably have to pay into workers' compensation. Here you can add your rates so we can calculate and remit your dues. You will still need to report insurable earnings to the workers' compensation board. If you are unsure what your WCB rate is, please check out the Canadian Centre for Occupational Health and Safety for more info.

To add a WCB rate, select Add rate and choose your:

  • Province
  • Account number (The number your provincial Workers compensation board gave you when you registered)
  • Rate (Rate is provided by the provincial workers' compensation board

When completed, select Done.

Note: You'll only see an option for Revenu Quebec info if your headquarters is in Quebec, or you add an employee who works in Quebec.

Add banking information

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Important: Please allow 2-4 business days after you have completed all three parts of the bank account validation for your account to be verified and ready to run payroll:

  • Micro-deposit verification
  • Cheque/ID upload
  • Yodlee verification

Note: Direct deposit, Workers compensation and source deductions will be withdrawn as a lump sum, and show on your bank statement as Intuit Trust Pay. You can view your invoices in the reports section.

  1. Add the Name & Email of the Authorized bank signing officer for the bank account being used. The authorized bank signing officer or authorized signatory should be set up as a Company admin with all access to the QBO account
  2. Select your Bank name from the drop down list, and enter your Transit number & Account number
  3. Choose the Account type (Business or Personal)
  4. The Authorized signing officer for the company should agree to the terms of the Pre-authorized debit plan agreement
  5. Upload the required documents - void cheque for the bank account and government issued photo ID of the authorized signing officer
  6. Sign in to your online banking account as the last verification step
  7. When completed, select Done
  8. You won't be able to run payroll until you complete the micro-deposit and Yodlee verification. (2-4 business days after setup)
    1. Check your bank account to get the test amount.
    2. Select the Gear icon at the top, then Payroll settings
    3. Select Bank Account
    4. Enter the Amount of the test transaction in the field provided
    5. Select Complete validation
    6. Select Verify Account
    7. Choose Get started in the pop-up screen
    8. Search for or select your bank institution from the list of options
    9. Enter your online banking credentials. The online banking credentials are not stored or saved
    10. Select the bank account you set up in Advanced Payroll
    11. Select Confirm
  9. The Risk & Compliance team reviews the information provided for your new bank account (2 - 4 business days after setup is completed).
  10. Once approved, the Run payroll button will be enabled

Note: Payroll needs to be processed three business days prior to the pay date. This means that the necessary funds must also be available in your bank account three days prior to pay day.

Add payroll settings

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This section has three tabs: Set up Pay groups, Income, and Deductions.

  1. Pay schedule - Add employees and contractor to pay groups. To help you get started we've automatically added some default groups.
    1. Select Add pay schedule
    2. You can choose from 5 frequencies: Weekly, Bi-weekly, Semi-monthly, Monthly, or Quarterly
    3. After choosing a Frequency, you can Name it in the field provided
    4. Select Done when completed
  2. Income type - Add the types of income you pay to employees or contractors. We've started you off with some common ones. You can also request a new income type if you don't see what you're looking for.

    To add an income:

      1. Select Add Income type
    1. Choose from the Income type drop-down list. You can customize how this list will show up on pay stubs by entering an Income name in the space provided
    2. If you look below, you will see if the income type selected is Taxable, Payable, Pensionable, or Insurable. These are CRA standard settings and you will not be able to change them

    To request a custom income type:

    1. Select Request custom income
    2. Enter the desired Income type name
    3. You can also select what taxes are applicable (CPP/QPP, EI, Federal Tax, Provincial Tax, Health tax applicable & payable)
    4. You can also choose which box (14/A, 40/L or Other) this income will show up on the T4/Releve form
    5. Enter any additional notes, and chose Send when completed
    6. You will receive an email indicating whether or not your request was added to the list

    NOTE:You can add a reoccurring income (bonus, overtime, holiday & vacation) to employees and contractors.

  3. Deductions/Benefits - Things like medical benefits or RRSP contributions that you deduct from employees or contractors' pay. You can also request a new deduction type if you don't see the one you're looking for.To add a new deduction:
    1. Select Add deduction/benefit
    2. Choose from the Deduction/benefit type drop-down list. You can customize how this will show up on pay stubs by entering a Deduction/benefit name in the space provided
    3. If you look below, you will see if the income type selected is Taxable, Pensionable, or Insurable. These are CRA standard settings and you will not be able to change them

    To request a custom deduction/benefit type:

    1. Select Request custom deduction. You'll be prompted with a text box to explain the deduction request.
    2. Select Send when completed
    3. You'll receive an email indicating whether or not your request was added to the list

    Once completed with this section, select Save or Back to task list.

Add employees and contractors

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In this section you can add employees & contractors that you paid earlier this tax year.

  1. When you click the Add button for this section, you'll see a pop-up window that allows you to add someone to your payroll
  2. Enter their NameLast name
  3. Select whether they are an Employee or a Contractor
  4. Choose Yes or No when asked "Have you paid this employee in 2017, either directly or using an accountant payroll service?"
  5. Select Add when completed
  6. You will now see several tabs across the screen:
    • ProfileName, Social Insurance Number (SIN), Date of Birth (DOB), Hire date, Address, Email, Phone
    • Employment: Compensation rate, Hours per week, Pay group, Departments, Locations, Job Titles, Workers' Compensation rateVacation policy
    • TaxesFederal TD-1 amount, Additional withholdings, Work location, Provincial TD1, Income Tax/CPP/EI Exempt
    • Direct DepositAdd Banking info for Employee's Direct Deposit - Deposit Priority, Bank, Transit Number, Account Number. (This is used for service fees & direct deposit)
    • IncomeIncome types, Amount, Frequency, Hours associated
    • DeductionsDeduction Type, Amount, Frequency, Employee contribution, Company Contribution
    • Year to DateEnter Year-to-date amounts paid in the current calendar year, prior to using Advanced Payroll powered by Wagepoint.You must enter all employee's YTD payroll history prior to running payroll.
  7. Enter the required information for each tab and select Save.

Map your chart of accounts

We created some default accounts for you to get things moving. All you need to do is choose your Bank account. You can drill down under each section if you want to check that everything is going to the right place in your QuickBooks Online accounts.

  1. Choose your Bank Account from the drop-down list. This is where we’ll show the payroll charges that come out of your bank account. You can also create a new account from this screen.
  2. Select the Advanced drop-down to see the top level pre-selected accounts.
  3. You can select  the top-level account to see all the sub accounts in it.
  4. You can change any accounts you want and choose Done when completed.

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Payroll clearing account After you run payroll, tax and direct deposit amounts show here until the pay run is processed.
Wages & earnings expenses The expense for things like regular pay, overtime, and commission that you pay to employees & contractors. New income/deductions will inherit the top-level setting and can be changed at any time.
Employee benefits expenses The expense for company contributions you pay into employee benefits like health plans or RRSP’s.
Payroll tax expenses The expense for the portion you pay for payroll taxes like CPP and EI.
Wages & earnings liabilities The liability for things like regular pay, overtime, and commission that you pay to employees & contractors. There is no top-level account for these liabilities.
Benefits & deductions liabilities The amounts you deduct from employees & the portion you pay for benefits like health plans & RRSP’s.
Payroll tax liabilities The amounts you deduct from employees & the portion you pay to CRA or Revenu Quebec for payroll taxes
Payroll subscription fees The taxes and fees you pay for using Advanced Payroll. There is no top-level account for the fees. Sales tax expenses is for folks with sales tax centre not on


  • If you have the sales tax centre turned on in QuickBooks Online, you will use the Sales tax on processing fees.
  • If the sales tax centre is not on, you will want to use Sales tax expenses.
  • If you’re unsure how to track debits or credits, please consult an accountant.

To make changes after setup:

  1. Select the Gear icon.
  2. Choose Payroll settings.
  3. Navigate to the Chart of accounts tab.

You'll see two separate journal entries for each pay run.

  • Journal Entry 1
    • Syncs to your QBO account on the day payroll is run
    • Debits the clearing accounts and credits the bank account.
  • Journal Entry 2
    • Syncs to your QBO account on the pay date
    • Credits the clearing account debits expenses and liabilities.

Next steps

Now that the initial setup is complete review the remaining pay & tax settings to verify your direct deposit, tax remittance, and workers compensation are set up correctly.

For more information, see our Advanced Payroll support hub.

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