Switching from QuickBooks Desktop Payroll in 2026
Intuit discontinued QuickBooks Desktop Payroll for new customers in 2024 and has been winding down existing accounts since. If you are still on QuickBooks Desktop Payroll, you are on a path that ends. This page is the cheapest-replacement playbook: QuickBooks Online Payroll for the QBO migration path, or OnPay/Patriot/Gusto for the leave-the-Intuit-ecosystem path.
Cheapest replacement options for QuickBooks Desktop Payroll customers
| Provider | 5 EE / mo | 10 EE / mo | Intuit relationship |
|---|---|---|---|
| Patriot Full Service | $57 | $77 | None. Standalone. |
| OnPay | $70 | $100 | None. Standalone. |
| Gusto Simple | $70 | $100 | None. Standalone. |
| Square Payroll | $65 | $95 | None. Standalone. |
| QuickBooks Online Payroll Core | $75 | $105 | Kept (bundle with QBO accounting). |
| Roll by ADP | $54 | $79 | None. Standalone. |
| Paychex Flex Essentials | $64 | $89 | None. Standalone. |
| ADP Run Essential | $99 | $119 | None. Standalone. |
Stay in the Intuit ecosystem or leave entirely
The first decision is whether to stay in the Intuit ecosystem (QuickBooks Online + QuickBooks Online Payroll) or leave (move payroll to OnPay/Gusto/Patriot and consider moving accounting to Xero, Wave, or FreshBooks).
Staying in Intuit is easier in the short term. The data transfer from QuickBooks Desktop to QuickBooks Online is well-trodden, Intuit provides free migration tools, and the QuickBooks Online Payroll product is essentially the modern version of what you have been using. The downside is higher monthly cost, mandatory cloud-only workflow, and continuing the Intuit relationship that just discontinued your prior product.
Leaving Intuit means choosing a payroll provider (OnPay, Gusto, Patriot, Square) and a separate accounting tool (Xero at $32/mo, Wave free, FreshBooks at $19/mo). The total stack cost is typically lower than staying with Intuit, but the migration effort is greater because both payroll and accounting move at once.
For a 5-employee business currently paying $70 for QuickBooks Desktop accounting + Payroll Basic, the comparison is:
- QuickBooks Online Plus + Online Payroll Core: $174/mo ($99 QBO + $75 payroll)
- Xero Established + OnPay: $102/mo ($32 Xero + $70 OnPay)
- Wave Accounting + Patriot Full Service: $57/mo ($0 Wave + $57 Patriot)
The Wave + Patriot stack is the cheapest combined option at $57/mo. The Xero + OnPay stack is mid-cost with strong UX. The Intuit-keeps-you stack is the most expensive.
What to export from QuickBooks Desktop Payroll before terminating
Before you cancel, export everything. QuickBooks Desktop Payroll history is yours and you should not lose access if Intuit changes its retention policy after you cancel.
Exports to capture: year-to-date Payroll Summary report for the current year, prior years' annual Payroll Summary reports for tax history, all employee profile data (name, address, SSN, W-4 elections, pay rate history), all current benefit and deduction setups, all year-end W-2 PDFs for prior years, all federal Form 941 and 940 filings for prior years (your QuickBooks copy), and the complete general ledger for any years where payroll data flowed into your accounting.
For the new payroll provider, the most important export is the current-year year-to-date wage and tax data per employee. The new provider needs this to issue a single year-end W-2 that covers the full year (the portion paid through QuickBooks plus the portion paid through the new provider).
If you choose to stay with Intuit
QuickBooks Online Payroll Core at $45 + $6 per employee is the direct Intuit upgrade path. Migration from QuickBooks Desktop Payroll is well-supported by Intuit and is often a guided service with no extra fee. Employee data, YTD wage data, and historical tax data move cleanly.
The trade-offs versus Desktop:
- Higher monthly cost ($45 + $6 versus the legacy $35 + $4)
- Web-only workflow (no offline access)
- Same-day direct deposit included (Desktop did not have this)
- Tighter integration with QuickBooks Online accounting (which you also need to migrate to)
For businesses that genuinely value the Intuit ecosystem and the QuickBooks Online accounting product, this is the rational path. For businesses choosing payroll provider on price alone, cheaper alternatives outside Intuit win on dollar cost.
OnPay for payroll + Wave for accounting as the cheap exit
For a QuickBooks Desktop user who wants to leave Intuit entirely and pay the lowest possible combined cost, the recommended stack is:
- Payroll: OnPay at $40 + $6 per employee (multi-state included, W-2 included)
- Accounting: Wave Accounting (free, no platform fee, payment processing fees on invoices)
- Combined cost at 5 employees: $70 per month
- Combined cost at 10 employees: $100 per month
The trade-offs versus QuickBooks: Wave's reporting is less deep than QuickBooks (acceptable for most SMBs, limiting for businesses with complex multi-class or departmental reporting needs). Wave's payment processing fees are higher than QuickBooks Payments. There is no native sync between OnPay payroll and Wave accounting; you import payroll journal entries to Wave monthly.
For most small businesses leaving QuickBooks Desktop, this trade-off is acceptable and the cost savings are real. The migration time investment is roughly 12 to 20 hours total across both systems, which is amortised over the first year of savings.
Other switching and cheap-vendor pages
Switching from ADP to cheaper
ADP Run exit mechanics
Switching from Paychex to cheaper
Paychex undisclosed-pricing exit
Cheapest QuickBooks Payroll plan
QBO Payroll Core breakdown
Cheapest OnPay plan
Flat $40 + $6, multi-state
Cheapest Patriot plan
$17 + $4 self-tax
Switching (existing)
General switching mechanics
Common questions
What happened to QuickBooks Desktop Payroll?
Intuit announced in 2024 that QuickBooks Desktop products were being sunset in favor of QuickBooks Online. QuickBooks Desktop Payroll specifically stopped accepting new subscriptions in 2024 and existing accounts are being migrated to QuickBooks Online Payroll on a rolling basis. Tax-table updates and customer support for Desktop Payroll are being maintained on a finite timeline.
Do I have to switch to QuickBooks Online Payroll?
No. You can switch to any payroll provider. QuickBooks Online Payroll is the closest replacement if you also use QuickBooks Desktop accounting. OnPay, Patriot Full Service, and Gusto are cheaper standalone payroll options if you are willing to handle the accounting integration manually or move accounting to a different tool too.
How much does QuickBooks Online Payroll cost compared to Desktop?
QuickBooks Online Payroll Core is $45 + $6 per employee, comparable to or slightly more than the old QuickBooks Desktop Payroll Basic at around $35 + $4. The price increase has been a sticking point for Desktop loyalists, and the cheaper alternatives outside Intuit are part of the reason many are looking.
Can I export my QuickBooks Desktop Payroll data?
Yes. QuickBooks Desktop has a payroll data export through the Reports menu (Payroll Summary and Employee Earnings Summary). Year-to-date wage and tax data exports cleanly to CSV or PDF. The new provider's migration team can use this directly.
What about QuickBooks Desktop accounting?
QuickBooks Desktop accounting (the non-payroll part) is also being phased out. Intuit's official position is that Desktop accounting will continue to be supported but with reduced feature development. If you are switching payroll anyway, this is a natural moment to evaluate whether to switch accounting to QBO, Xero, or Wave at the same time.
What is the cheapest payroll replacement for a 5-employee QuickBooks Desktop user?
Patriot Full Service at $57 per month is the cheapest done-for-you-tax option. QuickBooks Online Payroll Core at $75 keeps the Intuit relationship but costs $18 more. OnPay at $70 is the middle path. Gusto Simple at $70 wins on UX.