How to e-File a GST/HST Return Using QuickBooks or Other Software

Introduction

Filing your GST/HST return online has never been easier — especially when using modern accounting platforms such as QuickBooks Online, Xero, Sage, or Wave. These tools integrate directly with the Canada Revenue Agency’s (CRA) electronic filing system, allowing you to prepare, review, and submit your GST/HST returns in just a few clicks.

This step-by-step guide from Mackisen CPA Montreal explains how to e-file your GST/HST return safely and accurately using accounting software. You’ll also learn best practices for setup, reconciliation, and record retention to ensure full CRA compliance.

Legal and Regulatory Framework

The filing of electronic GST/HST returns is governed by the Excise Tax Act (R.S.C. 1985, c. E-15) and administered by the Canada Revenue Agency (CRA).

Electronic filing is mandatory for most GST/HST registrants with more than $1.5 million in annual taxable revenues and is strongly encouraged for smaller businesses.

Accepted electronic methods include:

• CRA’s My Business Account (MBA) portal.

• Direct e-file integration through approved accounting software (QuickBooks, Xero, Sage).

• CRA’s “NETFILE” web forms (for manual online submission).

Learning Insight

E-filing ensures faster refunds, immediate confirmation, and fewer paper errors. CRA considers the filing date to be the date your return is successfully transmitted, not when payment is made.

Step-by-Step: How to e-File GST/HST with QuickBooks

Step 1 — Verify Your GST/HST Setup in QuickBooks

Before filing, confirm that:

• Your GST/HST account is correctly registered and linked to your Business Number (BN) (format: 123456789RT0001).

• The reporting period (monthly, quarterly, or annual) matches CRA’s assigned schedule.

• The software’s tax codes (GST, HST, zero-rated, exempt) are properly configured.

Tip: In QuickBooks → Taxes → Sales Tax Settings, ensure “Agency: Canada Revenue Agency” is listed as the filing authority.

Step 2 — Reconcile Before Filing

Reconcile your GST/HST accounts to avoid inaccurate submissions:

• Match all invoices, payments, and credit notes for the filing period.

• Review Input Tax Credits (ITCs) — GST/HST paid on business expenses.

• Verify that your GST/HST Payable balance equals the system-calculated amount.

Learning Insight

CRA often audits discrepancies between GST collected and ITCs claimed. Monthly reconciliation minimizes the risk of reassessment.

Step 3 — Generate the Return

In QuickBooks:

1. Go to Taxes → Sales Tax → Prepare Return.

2. Choose your reporting period (e.g., Jan 1 – Mar 31, 2025).

3. Review the system-generated summary, including:

   • Line 101 — Total sales and other revenue.

   • Line 105 — GST/HST collected or collectible.

   • Line 108 — Input Tax Credits.

   • Line 109 — Net tax (line 105 – line 108).

4. Confirm accuracy and click File Return.

Step 4 — Connect to CRA’s Online Filing System

QuickBooks and other CRA-certified software use a secure Application Programming Interface (API) to connect directly to CRA’s servers.

When prompted:

• Sign in using your CRA My Business Account credentials or authorized access key.

• Grant permission for QuickBooks (or your software) to transmit your GST/HST return electronically.

• Review the pre-filled information and click Submit.

You’ll receive an immediate confirmation number from CRA — save or print it. This is your official proof of filing.

Step 5 — Make Your Payment

Even after e-filing, you must pay any balance owing separately.

Options:

• Online banking: add CRA GST/HST as a payee.

• Pre-authorized debit: set up payment within your CRA My Business Account.

• CRA My Payment: pay directly by debit card.

Record the payment confirmation in QuickBooks for reconciliation.

Step 6 — Store and Backup Records

Keep digital copies of:

• Filed return summaries and CRA confirmation numbers.

• Supporting transaction lists (sales, purchases, ITCs).

• Payment receipts and reconciliation reports.

Retention period: six years from the end of the fiscal year the return covers.

Learning Insight

QuickBooks allows you to attach supporting PDFs to each return. This feature is invaluable if CRA requests documentation later.

Using Other Accounting Software

Xero:

• Go to Accounting → Reports → GST/HST Return.

• Review the auto-filled fields and select File Now via CRA NETFILE.

• Save the confirmation page.

Sage Business Cloud:

• Access Taxes → GST/HST Report → Submit to CRA.

• Log in with your CRA credentials and transmit directly.

Wave Accounting:

• Generate the GST/HST summary report.

• File manually through CRA’s NETFILE portal by copying the values into the online form.

Common Mistakes to Avoid

• Filing without reconciling transactions.

• Selecting the wrong reporting period.

• Forgetting to click “Submit to CRA” after previewing the return.

• Assuming payment submission equals filing.

• Discarding the CRA confirmation number.

Learning Insight

Payment ≠ Filing. You must both submit the return and make payment to remain compliant.

Real Business Example

A Montreal tech consultant used QuickBooks to e-file quarterly GST/HST returns but forgot to reconcile refunds. CRA later requested backup records. With Mackisen CPA’s guidance, he re-filed corrected returns and received over $2,100 in refunded ITCs.

Another client manually keyed HST figures into CRA’s NETFILE instead of using the QuickBooks integration, introducing typos that caused reassessment. After switching to automated e-filing, accuracy improved and filing time dropped by 70%.

Lesson: e-filing saves time — but only when your books are properly reconciled.

Compliance Checklist

Do

• Verify CRA account setup and tax codes.

• Reconcile GST/HST before e-filing.

• Save CRA confirmation numbers.

• Pay balances electronically before due dates.

• Maintain records for six years.

Don’t

• Assume software submission replaces payment.

• File without verifying ITCs and sales totals.

• Lose confirmation pages or PDF reports.

• Mix multiple periods in one return.

Mackisen Strategy

At Mackisen CPA Montreal, we help businesses file GST/HST returns effortlessly by:

1. Setting up CRA e-filing credentials in QuickBooks, Xero, or Sage.

2. Performing pre-submission reconciliations.

3. Reviewing ITCs for missed credits.

4. Handling post-filing audits or adjustments.

Our CPA-supervised system ensures accurate, compliant, and audit-ready GST/HST submissions — every time.

Why Mackisen

With over 35 years of combined CPA expertise, Mackisen CPA Montreal helps small and medium-sized businesses across Quebec and Ontario modernize their GST/HST compliance. We simplify technology, improve accuracy, and safeguard your filings from errors or penalties.