Best Online Payroll Options for Small Organizations

Nonprofit organizations are increasingly turning to third-party providers for payroll. Using an online payroll service for your nonprofit’s employees is efficient, freeing up your time so that you can focus on the more important aspects of running your nonprofit, and cost-effective, while also offering additional benefits like ensuring your taxes will be filed correctly and on-time. We’ve detailed some online payroll services that are well-suited for smaller nonprofits with few employees.

Intuit Payroll

Why we like it: great for small nonprofits; three levels of payroll plans offers different options; no hidden costs; offers mobile access from your iPhone or Android 

Monthly base fees:

  • Basic: offers instant paychecks for W-2 employees, automatic guaranteed tax calculations, free direct deposit, free live support; no tax forms included – create reports for tax filings
    • $20/month for first 6 months, plus $2 per employee per month – after the first 6 months, monthly fee increases to $25/month
    • Enhanced: offers everything included in basic while also automatically filling out and completing your payroll tax forms (your taxes aren’t filed or paid for you, you still have to do this on your own). The package also offers email reminders for taxes and forms and the ability to print W-2 forms for your employees.
      • $31.20/month for the first 6 months, plus $2 per employee per month – after the first 6 months, monthly fee increases to $39/month.
      • Full Service: runs your payroll, handles all your payroll tax responsibilities, provides your year-end W-2 forms, and has someone set up the system for you
        • $79/month for the first 6 months, plus $2 per employee per month – after the first 6 months, monthly fee increases to $99/month
  • Additional fees and charges: Intuit also offers accounting software called QuickBooks, which you can be integrated with Intuit Payroll for more extensive services and an additional cost.

OnPay

    • Why we like it: ideal for nonprofits with fewer than 10 employees; easy to use; excellent customer service; very low-cost; offers mobile access from your iPhone or Android 
    • Includes: basic online payroll services, plus unlimited pay runs, instant on-site check printing, direct deposit, tax payments and filings done for you, and expert customer support 
    • Monthly base fee: $39.95 – includes service for up to 10 employees (note: most online payroll systems charge a fee per employee each month; OnPay is great for small businesses because it allows for 10 employees to be in the payroll service for no fee)
    • Additional fees and charges:
      • Additional $1 charge per employee after the first 10 employees
      • $8/month charge if you wish to pay your employees with direct deposit
      • If you have employees working in multiple states, there will be a $10/month fee for each additional state
      • $3.75 year-end fee, plus shipping, per employee for printing and mailing out W-2 forms (note: OnPay will report them to the state for you, now for no additional charge)

Gusto (formerly known as ZenPayroll)

  • Why we like it: offers a two-month free trial, which you can cancel anytime risk free; offers a lot of features; offers mobile access from your iPhone or Android
  • Includes: basic online payroll services, automatic tax processing, automated new hire reporting, employee self-enrollment, digital pay-stubs, ability to support hourly and salaried employees, detailed payroll reports, ability to cancel payroll, net-to-gross payments, direct deposit and checks, free online support, and more
  • Monthly base fee: $29, plus $6 per employee per month (note: Gusto considers an “employee” to mean anyone who receives a paycheck from your nonprofit – for example, this could be a freelancer you hire short-term, or an independent contractor)
  • Additional fees and charges: None. Unlike most other online payroll services we’ve seen, Gusto’s monthly price includes everything the service offers, including direct deposit, unlimited payroll runs, year-end W-2s and 1099s, new-hire reporting, and compliance management.

Wave Payroll

  • Why we like it: extremely low-cost; fast, simple online setup and free online support; offers mobile access from your iPhone or Android
  • Includes: basic online payroll services, plus streamlined year-end filling, easy-to-understand tax liabilities tracking, employee self-service portal for pay stubs and W2s, payroll reminders in your inbox, direct deposit and check printing, 256-bit SSL encryption and automatic backup, free email, phone, and online chat support
  • Monthly base fee: $15, plus $4 per employee per month (applicable for up to 100 employees; contact for enterprise pricing for over 100 employees)

Wagepoint

  • Why we like it: easy to use; simple, low-cost pricing; offers mobile access from iPhone and Android devices; offers a free trial available for 30 days
  • Includes: basic online payroll services, direct deposit, payroll calculations, federal, state, and local taxes, 1099s, W-2s, and Ws, wage detail reports, new hire reporting, payments to contractors, and online pay-stubs
  • Monthly base fee: $15, plus $2 per employee per month, including 10 state/local taxes
  • Additional fees and charges: additional states/local taxes at $2 per payee

Xero

  • Why we like it: no hidden costs; three levels of payment plans offers different options; offers mobile access from iPhone and Android devices
  • Includes: basic online payroll services, plus invoicing and quotes, bank reconciliation, inventory, 400+ third-party apps that integrate with Xero, bill and expense management, and more
  • Monthly base fee:
    • Starter: $9/month – create and send 5 invoices, enter 5 bills, reconcile 20 bank transactions, unlimited users
    • Standard: $30/month – all Starter plan features, plus payroll for 5 employees, federal and state e-file and e-pay, and payroll direct deposits and checks
    • Premium: $70/month – all Standard plan features, plus payroll for 10 employees and will deal with multiple currencies
  • Additional fees and charges: contact for quote for larger plans

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