Best Payroll Software for Accounting Firms (2026): Top 9 Compared

QuickBooks Workforce is Intuit's current name for its payroll line, and the accountant page is written for firms that run payroll for clients. Firms add payroll by signing in to QuickBooks Online Accountant. Three tiers are listed. Workforce Payroll covers full-service payroll with automated taxes and forms, next-day direct deposit and self-serve onboarding. Premium adds same-day direct deposit, expert setup and QuickBooks Time Premium. Elite adds QuickBooks Time Elite, project tracking, tax penalty protection and a personal HR advisor.

The page describes Intuit AI that gathers client attendance data and flags inconsistencies before a firm runs payroll, plus job costing and payroll reports for advisory work. Benefits such as health insurance, 401(k) plans and workers' compensation are available through integrations.

The billing options are the main reason firms compare it. A firm can pay for the client at 30% off for the life of the subscription, pass a 30% discount for the first 12 months to a client who pays directly, or enrol in the ProAdvisor Revenue Share Program. Firms whose clients do not use QuickBooks Online gain less from the integration.

Patriot Software sells online payroll and accounting to small businesses and runs a partner program for accountants and bookkeepers. The accountant page states there is no fee to partner. Discounts apply per client at five levels, from Bronze for one to five clients to Diamond for 100 or more, and the same discounts extend to the Time and Attendance and HR add-ons.

Basic Payroll includes unlimited payrolls, automatic payroll, contractor payments, free direct deposit and an employee portal. Full Service Payroll adds federal, state and local tax filings and deposits, year-end filings at no extra fee and a filing guarantee.

For the firm, Patriot offers consolidated billing at reduced rates so the practice can bill clients its own fee, free co-branding with the firm's logo and partner-only reports covering client tax settings, payroll schedules and employee payroll totals. Support is US-based by phone, email and chat. Once the firm has six or more active clients, Patriot payroll and accounting for the firm's own business are free.

SurePayroll, a Paychex company, runs a reseller program for accountants. The accountant page describes it as a white-label service: the firm sets up a custom portal with its logo and colours, can embed it on its own website and sends clients a link. Either the firm or the client can run payroll in the same portal.

Every client receives automated tax filing and deposits, free direct deposit, year-end W-2, W-3 and 1099-NEC processing, employee self-service, Auto-Payroll schedules, PTO tracking, on-demand reports and general ledger exports. The firm manages all client payrolls from one dashboard with role-based access for its staff.

SurePayroll states its pricing for resellers is wholesale with no long-term contract, and a firm can move clients one at a time. Onboarding help is free, and SurePayroll enters year-to-date data for new clients. The wholesale figures are not on the page, so a firm needs a quote to model its margin against the public $29 per month plus $7 per worker rate.

CheckMark has sold payroll software since 1984 and offers an online Accountant Edition for payroll firms, accountants and multi-company businesses in the United States. It includes everything in the Business Edition plus a single dashboard for unlimited client companies, dedicated onboarding assistance, priority US-based support and an employee self-service portal for client employees.

Features include unlimited payroll runs, multiple pay periods and pay rates, custom incomes, deductions and garnishments, PTO tracking, document management, custom admin permissions and more than 50 payroll reports. The software creates ACH direct deposit files that the firm submits to its bank, or prints MICR-encoded checks on blank stock. Forms 941, 940, 944, 943, W-2 and W-3 can be printed or e-filed.

This is a do-it-yourself product: the firm owns tax filing and deposits. The billing FAQ explains that each client company is charged a base fee in the month it is added, then the previous month's employee fees with each new base fee. A desktop version with separate multi-company licensing is also sold.

Drake Accounting is written for tax professionals who keep client books and run client payroll. The Professional Edition at $795 a year includes double-entry accounting with GAAP-compliant financials, live and after-the-fact payroll with multi-location support and batch processing, automatic journal posting, accounts payable and receivable with check printing, and financial reports. Direct deposit runs through NACHA files or Kotapay.

A second edition at $395 a year is aimed at firms focused on quarterly and annual payroll reporting. It supports direct entry of federal and state forms, generates W-2s, 1099s and all 94x forms, and includes federal and state e-filing.

Both editions have no limit on clients, installs or e-filing. Data exports to Drake Tax, and Drake Pay handles client payment collection. The software runs on Windows 11 and Windows Server, and can be networked from a shared drive. Clients cannot log in to run payroll themselves, so the model suits firms that process payroll for clients rather than with them.

ezPaycheck from Halfpricesoft is in-house payroll software that runs on Windows and Mac computers. The accountant page targets CPAs, accountants and payroll service providers with one flat annual rate for unlimited companies and employees and no monthly or per-employee fees.

The software supports daily, weekly, biweekly, semi-monthly and monthly pay periods, calculates federal, state and local taxes, and allows manual after-the-fact checks. It produces Forms W-2, W-3, 940, 941 and 943, handles deductions such as 401(k), health insurance and child support, and pays both W-2 employees and 1099 contractors. Forms 941 and 940 can be e-filed, and companion products such as ezW2 and ezACH extend it.

Data is stored locally and no internet connection is needed to run payroll. Halfpricesoft recommends up to 500 active employees per company file for performance. Licenses are annual because tax tables change, so a 2027 license is needed for 2027 payroll. The trade-off is that the firm handles every filing and deposit and clients have no online access.

Wagepoint describes itself as payroll software for bookkeepers and accountants in Canada. Its accountant page covers both managed payroll, where the firm runs pay, and client-run payroll, with the firm keeping visibility across every account.

One partner dashboard shows all clients with multi-admin access for the firm's team, and a client directory flags who needs help, connects existing Wagepoint clients or sets up new ones. Firms can make pay period and year-to-date adjustments, create custom income, deduction and benefit codes, and apply effective-dated changes without contacting support. Remittances and T4 and T4A slips are filed automatically at no extra cost. Employees use a self-serve portal to update banking details, complete TD1 forms and download paystubs. Reports include payroll registers, posting journals and workers' compensation reports.

Public plans are priced per month plus a fee per employee or contractor. A firm with clients outside Canada needs a different product for them.

Payroll Relief from AccountantsWorld is cloud payroll built for professional payroll processors; its brochure is now published on the IRIS Software Group website. The product page covers federal and all 50 states including local jurisdictions, unlimited pay types and deductions, contractors, certified payroll and departmental and job costing allocation for businesses with up to 1,000 employees.

Direct deposit, tax payment, tax filing and electronic child support run automatically, with calculation accuracy guaranteed. Firms can batch-approve payrolls, print checks in batch and, at year end, print, email, e-file and release W-2s and 1099s to employee portals in batch. Clients can be given anything from no access to nearly full access, and exception-based timesheets let clients enter hours themselves. The Payroll Snapshot shows upcoming payrolls, e-filing status and tax payments for all clients.

Payroll Relief integrates with QuickBooks, Creative Solutions, Sage and AccountantsWorld's Accounting Power, and exports a generic file for other ledgers. Pricing requires a sales conversation.

Accounting CS Payroll is the payroll component of Thomson Reuters Accounting CS, designed for accountants providing payroll services. Processing is batch-oriented with cross-client capability, and Thomson Reuters states that firms can increase the number of clients served without add-on modules or extra staff.

Setup can be standardised for new clients and employees. Time arrives through remote payroll utilities or spreadsheet imports. The form library covers W-2, W-2C, the 940, 941, 943, 944 and 945 families and their corrections, 1095-C and 1099. Payment options include pre-printed and remotely printed checks, direct deposit and PayCard. Built-in reports and a report designer sit alongside fee calculation and invoicing for the firm's payroll service.

Client payroll administrators approve data in NetClient CS portals, processed checks and reports post back to the portal, and employees view paystubs and W-2s and update W-4 details online. The software can be hosted through Virtual Office CS. Pricing requires a sales conversation.