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Head-to-head · Nonprofit Payroll Software

MIP Payroll vs QuickBooks Payroll

  • Updated Oct 2026
  • Both researched from official sources
  • 5 checks side by side
Higher score MIP Payroll #2 in Nonprofit Payroll Software 8.8/10 Pricing on request ✓ 4 of 5 features Visit MIP Payroll
QuickBooks Payroll #8 in Nonprofit Payroll Software 6.9/10 30-day trial Free trial✓ 2 of 5 features Visit QuickBooks

MIP Payroll leads on 0 checks, QuickBooks Payroll on 0, and 5 are even. Who comes out ahead on the 5 yes/no, price and count checks where we have data for both products. The editor score weighs everything else too.

Our verdict

  • Highest scoreMIP Payroll · 8.8/10
  • Free trialonly QuickBooks Payroll
  • Most featuresMIP Payroll · 4 of 5

MIP Payroll scores higher on our rubric for nonprofit payroll software: 8.8 against 6.9 out of 10; our editors rank them #2 and #8.

MIP Payroll is the better fit for nonprofits needing fund-accounted payroll. QuickBooks Payroll is the better fit for quickBooks-centered nonprofits.

  • MIP Payroll fits best

    Nonprofits needing fund-accounted payroll

  • QuickBooks Payroll fits best

    QuickBooks-centered nonprofits

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Side by side

Feature MIP Payroll 8.8/10 Visit ↗ QuickBooks Payroll 6.9/10 Visit ↗
At a glance
Editor score 8.8 6.9
Ranking #2 in Nonprofit Payroll Software #8 in Nonprofit Payroll Software
Best for Nonprofits needing fund-accounted payroll QuickBooks-centered nonprofits
Pricing model Paid Paid
Starting price Pricing on request $50/mo
Free plan Not checked yet —
Free trial — 30 days
Deployment Cloud, Self-hosted Cloud, Mobile
Platforms Web Web, iOS, Android
Features MIP Payroll 4/5 · QuickBooks Payroll 2/5
Tax filing included ✓ ✓
Nonprofit tax support ✓ (best) Not checked yet
Multi-state payroll ✓ ✓
Contractor payments Not checked yet Not checked yet
Time tracking ✓ (best) Not checked yet
Specs
Employee limit Not checked yet Not checked yet
Our review
Pros
  • Allocates payroll costs by program, department, or grant
  • Supports federal and state tax reporting with W-2/W-3 e-filing
  • Offers payroll groups, timesheets, direct deposit, and custom payroll codes
  • Automates payroll tax calculations, filings, and payments
  • Provides direct deposit and employee self-service portals
  • Connects with QuickBooks Online, Square, and benefits platforms
Cons
  • Pricing requires a demo or sales contact
  • Integration centers on MIP Accounting
  • Cloud and on-premise options add deployment decisions
  • Higher-tier plans are needed for time tracking and scheduling
  • The product is designed for small businesses, not only nonprofits
  • Less suited to buyers prioritizing tip management or one payroll frequency
Our verdict

MIP Payroll is a payroll module within MIP Accounting, a fund accounting system designed for nonprofits, schools, healthcare organizations, and government entities. Its strongest fit is for organizations that need payroll records and…

Read the review →

QuickBooks Payroll is a cloud payroll service for small businesses, including nonprofits that already work in the QuickBooks ecosystem. It calculates, files, and pays payroll taxes; supports direct deposit; provides employee portals for…

Read the review →
  1. MIP PayrollNonprofit Payroll Software 8.8Pricing on request
  2. QuickBooks PayrollNonprofit Payroll Software 6.930-day trial

Strengths and trade-offs

  • MIP Payroll — where it wins

    • Allocates payroll costs by program, department, or grant
    • Supports federal and state tax reporting with W-2/W-3 e-filing
    • Offers payroll groups, timesheets, direct deposit, and custom payroll codes

    Where it doesn't

    • Pricing requires a demo or sales contact
    • Integration centers on MIP Accounting
    • Cloud and on-premise options add deployment decisions

  • QuickBooks Payroll — where it wins

    • Automates payroll tax calculations, filings, and payments
    • Provides direct deposit and employee self-service portals
    • Connects with QuickBooks Online, Square, and benefits platforms

    Where it doesn't

    • Higher-tier plans are needed for time tracking and scheduling
    • The product is designed for small businesses, not only nonprofits
    • Less suited to buyers prioritizing tip management or one payroll frequency

More comparisons

All nonprofit payroll software comparisons → · Full ranking →

Reviewed by iTechGuides Editors · Editorial team · Updated Oct 2026

Last updated · How we research and update