How to e-File a GST/HST Return Using QuickBooks or Other Software — Montreal CPA Firm

Modern accounting software like QuickBooks, Xero, Sage, and Wave makes filing GST/HST returns easier — but only if the system is configured properly. Many entrepreneurs assume their software automatically records tax correctly. It doesn’t. If your tax codes, account mappings, or report settings are wrong, your filings will contain errors that CRA can easily detect. This guide explains how to safely e-file your GST/HST return using accounting software, based on the precision-based filing process Mackisen uses for clients.

Why Software-Based Filing Matters
Using software reduces manual entry, ensures accurate calculations, and automates reconciliation — but only if tax codes and accounts are set up correctly. Incorrect setup leads to incorrect GST collected numbers, incorrect ITCs, and incorrect net tax.

Legal and Regulatory Framework
CRA requires accuracy under the Excise Tax Act. Hickman Motors (1997) confirms that taxpayers must prove correctness, even if software performed the calculation. The GST/HST Electronic Filing Regulations govern e-filing requirements.

The Software Setup Disaster
Imagine filing your GST return directly through QuickBooks. Everything looks correct — until CRA reviews your return and discovers that your “GST on Sales” account includes exempt transactions incorrectly coded as taxable. Your refund is frozen. CRA demands invoices. You discover your software setup was wrong for an entire year. You now need to amend multiple periods and justify discrepancies. This scenario is extremely common.

Learning Section: Software Basics You Must Understand
Tax codes determine how GST/HST behaves
Sales accounts must be mapped correctly
ITCs must be assigned to eligible expenses
Zero-rated items must be coded properly
Imports and out-of-province purchases may require manual adjustments
You must verify every tax code manually.

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How to e-File GST/HST Properly Using Software
Step 1: Review your sales accounts
Step 2: Review tax codes (ensure only taxable items include GST/HST)
Step 3: Reconcile GST collected vs. sales
Step 4: Review ITCs on all expenses
Step 5: Run the GST/HST Summary Report
Step 6: Compare software totals to bank/merchant statements
Step 7: File electronically through CRA
Step 8: Save confirmation and attach to your reconciliation package

Documentation Section
GST/HST Summary Reports
Tax code configuration screenshots
Invoices and receipts
Proof of payment
Monthly reconciliations
Export logs for zero-rated items
Keep all documents for six years.

Common Mistakes
Incorrectly coded transactions
Mixing exempt and taxable sales
Claiming ITCs without documentation
Failing to reconcile
Using default U.S. tax codes
Not accounting for digital sales properly

Winning With Revenue Québec and Canada
Mackisen audits your accounting software’s tax setup, corrects mappings, identifies miscoded transactions, reconciles accounts, and prepares a full GST filing binder before submission.

Mackisen Service Hub
We manage software-based GST filing, tax code setup, reconciliation, CRA inquiry responses, and refund management.

Why Mackisen
With over 35 years of tax and software expertise, Mackisen ensures your GST/HST filings are accurate, compliant, and fully supported by documentation — no matter which accounting platform you use.