The real cost of running payroll on Wave, QuickBooks, and Wagepoint in 2026

The sticker price of payroll software in Canada looks cheap: $20 to $40 a month plus a few dollars per employee. But that number hides the real cost.

You’re paying for an accounting tool and a separate payroll tool that don’t talk to each other, plus the hours (or the bookkeeper) it takes to reconcile the two every month. Once you add it up, a four-person business is often spending $1,400–$2,500+ a year on the stack, and most of that isn’t the payroll fee. It’s the seam between the tools.

What does each option actually cost in 2026?

Here’s the honest breakdown for a small incorporated business running payroll for a handful of people. All prices are Canadian, per month, before tax.

Setup	Accounting	Payroll	The catch
QuickBooks Online + Payroll	$70 (Essentials) to $110 (Plus)	Core $30 base + $5/employee (Premium $55 + $8; Elite $80 + $15)	Two products to reconcile; payroll syncs to your books but often lands in the wrong spot
Wave + Wave Payroll	Starter free; automatic bank-feed imports are Pro-only at $25/mo	$25 base + $6/active employee	Not available in Quebec at all: Wave remits to the CRA only, not Revenu Québec; support is chat-only on lower tiers
Xero + Wagepoint (or Rise)	$60 (Standard)	No native Canadian payroll: bolt on Wagepoint at $20 + $4/payee (Solo) or $40 + $6/payee (Unlimited)	You’re the integrator: two vendors, two logins, one reconciliation
FreshBooks + payroll partner	$42 (Plus)	No native Canadian payroll: offered through a PaymentEvolution partnership, pricing unpublished	Built for invoicing; payroll means adding another vendor once you have employees

Competitor prices verified as of August 2026 and sourced below. Watch the per-employee line especially: Intuit’s introductory promos discount the base subscription but never the per-employee fee, so the “half off” price you sign up at isn’t the price you pay per head. SaaS pricing changes often, so verify with each vendor before relying on these figures.

The number the price page doesn’t show

Say you’re a four-person shop on QuickBooks Online Plus + Payroll Core. Your software bill is $110 + $30 + (4 × $5) = $160/month, or roughly $1,900 a year. On the leaner Essentials plan it’s $70 + $30 + $20 = $120/month, about $1,440 a year. Not bad, on paper.

Now add what the software doesn’t do:

• The reconciliation. Every month, the payroll run has to be matched back into the books. When they don’t agree (and they routinely don’t), someone fixes it by hand.
• The bookkeeper. For a lot of owners, “someone” is a bookkeeper at $400–$600/month. Call it $550: that’s $6,600 a year, and a big chunk of it is spent re-doing entries that should have posted correctly the first time.
• The year-end cleanup. The accountant who untangles it all in April bills for the untangling. For a stack like this, a ~$4,200 year-end bill is normal.
• Your time. Even with help, you’re still the one screenshotting sales tax and re-keying the payroll numbers that didn’t match. Call it a couple of hours most weeks. At even $60 an hour, that’s ~$6,240 a year, plus a scramble every April.
• The misses. One payroll remittance that goes out late because it lived in the other tool: ~$500 in interest and penalties.

Add it up: $6,600 + $4,200 + $6,240 + $500 ≈ $17,500 a year on top of the software bill. Depending on your bookkeeper’s rate and how much you do yourself, the real annual cost of the stack for a small team typically lands at $15,000–$18,000, and the payroll fee is the smallest line on it. You’re not paying for payroll. You’re paying for the gap between payroll and your books.

Why does the gap exist at all?

None of these tools are bad at what they do. The problem is structural: accounting and payroll are two different products, sometimes from two different companies, and the “integration” between them is a sync: an import, a mapping, a monthly reconciliation.

Every sync is a place for the numbers to drift. Xero doesn’t even offer Canadian payroll, so you have to bolt on a second vendor. Wave and QuickBooks bundle it, but it’s still a separate module posting across a seam.

That seam is the product you’re actually paying to maintain.

See what one login instead of three looks like. Countet runs payroll and your books as one system: the numbers can’t drift because there’s nothing to sync. Start free →

The alternative: one system, no seam

The way to make the real cost go down isn’t a cheaper payroll add-on. It’s removing the reconciliation entirely.

Countet runs payroll and the books as one system. When you run payroll, the wages, the CPP/EI/tax deductions, and the cash all land in your books in the same moment: correctly, in the right place, with no export, no import, and nothing to re-fix. Payroll is included, not a separate base fee plus per-employee surcharge stacked on a separate product. T4s, T4As, and ROEs come from data that’s already there.

Countet’s own pricing reflects that: Solo is $79/month flat, payroll included, with a 30-day free trial, not a second product with its own base fee.

The result isn’t just a smaller software bill. It’s the bookkeeper hours you stop paying for, and the April you stop dreading.

If you’re adding up your own stack right now and the total is bigger than you expected, that’s the point. For a side-by-side on the accounting half, see our Countet vs. QuickBooks comparison.