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APS Payroll vs Microkeeper: Which Payroll Software Is Better?


Disclosure: We may earn commissions if you shop through the links below.

Last Updated: May 22, 2025

Both APS Payroll and Microkeeper are leading payroll software solutions, but which one is better for you and your business?

Below we compare APS Payroll and Microkeeper across nearly 50 different data points to help you make find the right one.

 

APS Payroll vs Microkeeper Reviews

APS PayrollMicrokeeper
Trustpilot Rating03.6
Number of Trustpilot Reviews096
iPhone App Rating44.4
Number of iPhone App Reviews135111
Android App Rating3.80
Number of Android App Reviews3570

APS Payroll vs Microkeeper Pricing

APS PayrollMicrokeeper
Free Trialn/aYes
Free Trial Lengthn/a1 month
Cheapest Plan NamePayrollPayroll & STP only
Cheapest Plan Cost Per Month$By request$28
Mid Priced Plan NamePayroll + AttendanceStandard
Mid Priced Plan Cost Per Month$By request$28
Top Plan NamePayroll + HR + AttendancePremium
Top Plan Cost Per Month$By request$150

APS Payroll vs Microkeeper Features

FeaturesAPS PayrollMicrokeeper
Target Business SizeMid size businessEnterprise
Unlimited Payrolls✘✘
Automated Tax Filing & Payments✔✘
E-sign I-9 & W-4✘✘
Live Customer Support✔✘
Third-Party Integrations✔✔
Ability To Manage Employee Benefits✔✔
Employee Access To Platform✔✔
Direct Deposit✔✔
Expense Reimbursement✘✘
Time Off Accrual✔✔
Pre-Tax Deductions✔✔
Wage Garnishment✔✔
Background Checks✘✘
Check Printing✔✔
Check Delivery✔✘
API✘✔

APS Payroll Payroll Features

  • Payroll Console
  • Guaranteed Tax Compliance – Federal and One State
  • Report Manager
  • Accrual Time Tracking
  • Employee Directory
  • Quarterly Tax Filings
  • New Hire Reporting
  • Direct Deposit and Paycards
  • General Ledger Reporting
  • Garnishment Processing
  • Multi-Account Management Center
  • Manager and Employee Self Service
  • Custom Report Builder
  • Custom Report Sharing
  • Existing Imports, Exports, and Integrations
  • Help Center
  • Unlimited Form W-2 Reprints Through APS
  • Unlimited Custom Fields
  • Payroll Batch Error Checking

Microkeeper Payroll & STP only Features

  • Payroll Processing
  • Leave
  • Public Holidays
  • Super Calculations
  • Employee Self Service Console
  • Paperless Employee Onboarding
  • Internal Messaging
  • Employee File Storage
  • Custom Reports
  • Native Xero Integration
  • MYOB / Sage / … Integration
  • Single Touch Payroll Compliance
  • 9-5 Email Support
  • 9-5 Phone Support

APS Payroll Payroll + HR + Attendance Features

  • HR Console
  • Performance Management
  • Employee Notification Center – Newsfeed, Email, and Text
  • HR Support Center
  • Asset Tracking
  • Training Course Enrollment and Tracking
  • Total Compensation Reporting
  • Document Management with eSignatures
  • Data Integrity Validation
  • OSHA Tracking and Reporting
  • Event Tracking
  • EEO and VETS 100a Reporting

Microkeeper Premium Features

  • Payroll Processing
  • Leave
  • Automated Award Application
  • Public Holidays
  • Super Calculations
  • SMS Rosters
  • iCal, Google Calendar, Outlook Export
  • Push Notifications
  • Print Export
  • Roster Confirmation
  • AutoRoster (Automated Shift Sheduling)
  • Shift bidding
  • Facial Recognition
  • Fingerprint Clocking
  • NFC Tag Clocking
  • GPS Clocking On Smart Device
  • Timesheet Tick Approval
  • Timesheet vs Roster Comparison
  • Employee Self Service Console
  • Paperless Employee Onboarding
  • Internal Messaging
  • Employee File Storage
  • Skills Matrix
  • Custom Reports
  • Native Xero Integration
  • MYOB / Sage / … Integration
  • Single Touch Payroll Compliance
  • Super Clearing House
  • 9-5 Email Support
  • 9-5 Phone Support

APS Payroll vs Microkeeper Pro & Cons

APS PayrollMicrokeeper
Pros
  • Customer Service
  • User Friendly
  • Easy Processes
  • Reporting
  • User Interface
  • 100% Australia Focused
  • Good UX
  • Great tech support
  • Budget-friendly (only for payroll only and standard packages)
  • Updates and information about governmental requirements
  • All-in-one solution
Cons
  • Reporting Issues
  • Technical Issues
  • Need Improvements
  • Not User Friendly
  • Adjustment Issues
  • Reporting could use significant improvement
  • Integration with platforms such as MYOB isn’t seamless and is prone to error
  • Limited employee dashboard
  • Pricey premium package that only seems to be targeting big businesses
  • Starter plan is pretty useless

Other Payroll Software Comparisons

  • Trolley vs Workday
  • OnPay vs Razorpay
  • Xero Payroll vs Zelt
  • Kashflow Payroll vs Inova Payroll
  • Paylocity vs Paymate
  • Payfit vs HRONE
  • Paycom vs CAVU HCM
  • Arbonum vs EBS PaySuite
  • Paycom vs Microkeeper
  • Justworks vs Excelforce

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