If you’re choosing payroll, you’re really choosing between Gusto and QuickBooks. They dominate the small business payroll market, and for good reason — both are excellent. But they approach payroll from fundamentally different angles, and the wrong choice means paying for features you don’t need or missing features you do.

Here’s the straight comparison.

The Short Version

• Choose Gusto if you want the best payroll experience and don’t mind it being separate from your accounting.
• Choose QuickBooks Payroll if you already use QuickBooks for accounting and want everything in one system.

Setup and Onboarding: Gusto Wins

Gusto’s onboarding is the gold standard. Enter your company info, add employees, connect your bank, and you’re running payroll. Most businesses complete setup in under an hour. Gusto also auto-files taxes in all 50 states.

QuickBooks Payroll setup is good but more complex, especially if you’re also setting up QuickBooks accounting for the first time. If you’re already using QuickBooks, adding payroll is straightforward. If you’re not, it’s a heavier lift.

Verdict: Gusto for speed. QuickBooks if you’re already in the ecosystem.

Payroll Features: Tie (Different Strengths)

Gusto handles:

• Full-service payroll (all 50 states)
• Automatic tax filing and payments
• Employee self-service portal
• Direct deposit (next-day available)
• Garnishments and deductions
• Contractor payments
• W-2 and 1099 filing
• Health insurance and 401(k) administration
• Workers’ comp
• PTO policies and tracking

QuickBooks Payroll handles:

• Full-service payroll (all 50 states)
• Automatic tax filing and payments (Core and Premium)
• Employee self-service portal
• Same-day direct deposit (Premium and Elite)
• Time tracking integration (QuickBooks Time)
• Workers’ comp
• W-2 and 1099 filing
• Health benefits (through third-party partners)
• 401(k) (through Guideline)

Both cover the essentials well. Gusto has more built-in benefits. QuickBooks has deeper time tracking integration.

Verdict: Tie. Both handle full-service payroll. Gusto wins on benefits. QuickBooks wins on time tracking.

Pricing: Gusto Wins for Small Teams

Gusto is cheaper at every tier for small teams. For a 5-employee business:

• Gusto Simple: $70/month
• QuickBooks Core: $75/month

For a 10-employee business:

• Gusto Plus: $150/month
• QuickBooks Premium: $155/month

Important caveat: QuickBooks Payroll requires QuickBooks Online accounting. If you’re not already paying for QBO ($30-90/month), the total cost is higher.

Verdict: Gusto on base payroll pricing. QuickBooks if you already use QBO (payroll is often discounted as an add-on).

Benefits Administration: Gusto Wins

Gusto is a benefits broker. They help you find, set up, and manage health insurance, 401(k), 529 plans, and commuter benefits — all through their platform. Gusto’s benefits team handles enrollment, compliance, and carrier communication.

QuickBooks Payroll offers health insurance and 401(k) through third-party partners (not directly). The integration works, but it’s less seamless.

Verdict: Gusto, clearly, if benefits are a priority.

Integration with Accounting: QuickBooks Wins

This is QuickBooks Payroll’s biggest advantage. If you use QuickBooks Online for accounting, adding payroll means:

• Payroll data flows automatically into your books
• No manual journal entries for payroll
• Tax liabilities appear in your chart of accounts
• Job costing includes labor costs
• One login for everything

Gusto integrates with QuickBooks, Xero, and FreshBooks, but it’s still a separate system. Transactions sync, but you manage payroll in Gusto and accounting in QuickBooks.

Verdict: QuickBooks if you want one system. Gusto if you don’t mind two systems that sync.

HR Features: Gusto Wins

Gusto includes HR features at every tier:

• Hiring and onboarding tools
• Offer letter templates and e-signature
• Employee directory and org chart
• PTO policies and tracking
• Employee surveys (Gusto Plus and Premium)
• HR resource library
• Compliance alerts

QuickBooks Payroll added HR features, but they’re less comprehensive and require higher-tier plans.

Verdict: Gusto for HR functionality.

Contractor Payments: Tie

Both handle contractor payments well:

• Gusto: Contractor payments, 1099 filing, and tracking included
• QuickBooks: Contractor payments, 1099 filing, and expense tracking included

Verdict: Tie. Both handle contractors effectively.

Customer Support: QuickBooks Wins (On Premium Tiers)

Gusto offers phone, chat, and email support on all plans. Response times are generally good, but phone support can have wait times during peak seasons.

QuickBooks Payroll offers phone support on all payroll plans, with priority support on Premium and Elite. QuickBooks also has a massive knowledge base and community forum.

Verdict: QuickBooks for support breadth. Gusto for consistent quality across plans.

The Decision Matrix

Our Recommendation

If you already use QuickBooks Online for accounting, add QuickBooks Payroll. The integration is seamless — payroll data flows into your books without manual entry. You manage everything in one system, and your accountant will thank you.

If you don’t use QuickBooks for accounting, choose Gusto. It’s the better payroll experience: easier setup, better benefits, more HR features, and lower pricing for small teams. Pair it with QuickBooks, Xero, or FreshBooks for accounting and you’ll have a more flexible system than QuickBooks Payroll alone.

Both are excellent. Neither is wrong. Pick based on whether you want one system (QuickBooks) or the best standalone payroll (Gusto).

SoftDecide helps churches, nonprofits, and small organizations find the right software. Our comparisons are independently researched. We may earn a commission if you purchase through links on this page — at no extra cost to you.