---
description: Compare Paychex Flex vs Microkeeper to learn about each of the product's price, benefits and disadvantages. Choose the best software for your business in Australia.
image: https://gdm-localsites-assets-gfprod.imgix.net/images/capterra/og_logo-e5a8c001ed0bd1bb922639230fcea71a.png?auto=format%2Cenhance%2Ccompress
title: Paychex Flex vs Microkeeper Comparison - Capterra Australia 2026
---

Breadcrumb: [Home](/) > [Direct Deposit Payroll Software](/directory/32598/direct-deposit-payroll/software) > [Paychex Flex \<span\>vs\</span\> Microkeeper](https://www.capterra.com.au/compare/119841/176357/paychex-flex/vs/microkeeper)

# Compare Paychex Flex vs Microkeeper

Canonical: https://www.capterra.com.au/compare/119841/176357/paychex-flex/vs/microkeeper

> Detailed comparison between Paychex Flex and Microkeeper. Check ratings, reviews, pricing, and features to make the best decision for your business.

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## At a Glance

| Metric | Paychex Flex | Microkeeper |
| **Overall rating** | 4.2/5 | 4.4/5 |
| **Total Reviews** | 1786 | 20 |
| **Starting Price** | - | USD 2.25 |
| **Free Trial** | No | Yes |
| **Free Version** | No | No |
| **Deployment** | Cloud, SaaS, Web-based, Mac (Desktop), Windows (Desktop), Android (Mobile), iPhone (Mobile), iPad (Mobile) | Cloud, SaaS, Web-based, Linux (On-Premise), Android (Mobile), iPhone (Mobile), iPad (Mobile) |
| **Support** | Email/Help Desk, Phone Support, 24/7 (Live rep), Chat | Email/Help Desk, FAQs/Forum, Knowledge Base, Phone Support, Chat |
| **Training** | In Person, Live Online, Webinars, Documentation | Live Online, Documentation, Videos |

## Best for

### Paychex Flex

Business Owners, Human Resources Professionals, CRHOs, CEOs, CFOs, of all business sizes use Paychex for HR, payroll, and benefits solutions to streamline and automate HR administrative tasks.

### Microkeeper

Australian businesses of all shapes and sizes (10 - 5,000 employees).&#10;Popular with Commercial Cleaning, Retail, Hospitality, Medical Clinics, Manufacturing, Consumer Industries and Agriculture.

## Key features

### Paychex Flex

- API
- Access Controls/Permissions
- Benefits Management
- Biometric Recognition
- Calendar Management
- Check Printing
- Clock In/Out
- Customizable Reports
- Direct Deposit
- Document Management
- Employee Scheduling
- Multi-Location
- Overtime Calculation
- Payroll Management
- Real-Time Data
- Reminders
- Reporting/Analytics
- Time Tracking
- Timesheet Management
- Wage Garnishment

### Microkeeper

- API
- Access Controls/Permissions
- Benefits Management
- Biometric Recognition
- Calendar Management
- Check Printing
- Clock In/Out
- Customizable Reports
- Direct Deposit
- Document Management
- Employee Scheduling
- Multi-Location
- Overtime Calculation
- Payroll Management
- Real-Time Data
- Reminders
- Reporting/Analytics
- Time Tracking
- Timesheet Management
- Wage Garnishment

## Links

- [View Paychex Flex Profile](https://www.capterra.com.au/software/119841/paychex-flex)
- [View Microkeeper Profile](https://www.capterra.com.au/software/176357/microkeeper)
- [View Original Comparison](https://www.capterra.com.au/compare/119841/176357/paychex-flex/vs/microkeeper)

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