How to Pay an Invoice in Canada: Methods, Costs and Checks

Someone has sent you an invoice and you want to pay it properly — on time, with a record, and without accidentally paying twice or paying the wrong account.

Here is what each payment method actually costs you, how long it really takes, and the checks worth doing before the money leaves.

Check these four things first

Before paying anything, especially a first invoice from a new supplier:

Does the invoice match what you agreed? Quote, purchase order, or the email where you approved the work.
Is the GST/HST right? If they are charging it, their business number should be on the invoice. No number, no tax — see what is required on an invoice in Canada.
Have you paid it already? Duplicate invoice numbers and re-sent reminders cause more double payments than fraud does.
Did the banking details change? If an email says an account has changed, phone the supplier on a number you already had. This is the single most common invoice fraud in Canada.

A changed bank account arriving by email is a red flag until you have confirmed it by voice on a number you looked up yourself — never the number in the email.

The methods, and what they really cost

Method	Speed	Cost	Best for
Interac e-Transfer	Minutes	Free to about $1.50	Amounts under the daily limit; most small suppliers
Bill payment (payee list)	1–3 business days	Free	Utilities, CRA, big vendors already in the list
EFT / direct deposit	1–3 business days	Low, often bundled	Regular suppliers, payroll-style runs
Credit card	Instant	Free to you; ~2–3% to them	When they offer a Pay Now button
Wire	Same or next day	$15–$30	Large or international payments
Cheque	Days, plus post	Cheque cost	When the supplier insists

E-transfer limits catch people out on bigger invoices — most banks cap somewhere around $3,000 a day and $10,000 a week, and the caps differ per bank and per account. For anything larger, EFT or a wire is the sane route rather than three transfers over three days.

Always put the invoice number on the payment

Whatever method you use, put the invoice number in the reference or message field. It costs three seconds and prevents the most common bookkeeping mess: a payment landing in the supplier's account that nobody can match to a bill, so they chase you for an invoice you have already paid.

If you are paying late

Say so, briefly, before the due date rather than after it. "This is going out on the 14th" is a normal business message that costs you nothing and buys real goodwill. Silence is what turns a late payment into a relationship problem — and eventually into the escalation ladder from the other side.

If the invoice carries interest terms you agreed to, expect them to be applied. Interest can only be charged if it was agreed beforehand, so check the engagement letter before disputing it.

Keep the record the CRA expects

For any business expense you plan to claim, keep the invoice itself, not just the bank line. The CRA wants records that show what was bought, from whom, when, and how much tax was charged — a payment confirmation alone does not show the GST/HST you are claiming back as an input tax credit.

Six years is the retention rule, counted from the end of the tax year the record relates to. Digital copies are fine, provided they are readable and complete.

Paying the CRA specifically

CRA payments do not work like supplier invoices. Use My Business Account, your bank's bill-payment list (the CRA appears as a payee), or a pre-authorised debit — and pick the right account, since GST/HST, payroll and corporate tax are separate. Money paid against the wrong account is genuinely tedious to reallocate.

General information for Canadian businesses, not financial advice. Bank fees, transfer limits and CRA payment options change — confirm current details with your bank or accountant.