Cliniko vs Deputy

Cliniko vs Deputy: Side-by-Side Feature & Pricing Comparison

An honest comparison of Cliniko and Deputy for Australian mid-market Australian businesses. See feature ratings, pricing, pros and cons to make the right choice - or let our Harvard-educated experts help you decide.

Features compared

50+

Clients advised

98%

Client retention

12+

Years experience

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Feature Comparison

Side-by-side feature analysis for Cliniko and Deputy.

Industry fit

Cliniko

Cliniko provides industry fit functionality, popular with Healthcare & Allied Health businesses

Deputy

Deputy provides industry fit functionality, popular with Hospitality & Tourism businesses

Both platforms cover the industry fit basics. The edges - automations, reporting depth, mobile parity - are where their opinions show.

Job management

Cliniko

Limitation: Inventory management for product sales (supplements, braces, etc.) is basic and requires workarounds or third-party tools

Deputy

Tasking module assigns and tracks tasks across locations, adding basic operational management beyond just scheduling

Deputy highlights job management as a core strength. Cliniko offers the capability but does not position it as a primary differentiator.

Quoting and invoicing

Cliniko

Cliniko provides quoting and invoicing functionality, popular with Healthcare & Allied Health businesses

Deputy

Deputy provides quoting and invoicing functionality, popular with Hospitality & Tourism businesses

quoting and invoicing capabilities vary by plan tier on both platforms. Confirm the specific features you need are available at your target price point before committing.

Scheduling and dispatch

Cliniko

Cliniko provides scheduling and dispatch functionality, popular with Healthcare & Allied Health businesses

Deputy

Drag-and-drop shift scheduling with templates and auto-scheduling saves hours of roster creation for multi-location businesses

Deputy highlights scheduling and dispatch as a core strength. Cliniko offers the capability but does not position it as a primary differentiator.

Mobile field access

Cliniko

Letter and report templates with merge fields generate professional referral letters and clinical reports in seconds

Deputy

Employee mobile app allows staff to clock in and out with GPS verification, swap shifts, and request leave without manager involvement

Both platforms are strong here. Cliniko emphasises this as a core strength, and Deputy also invests heavily in mobile field access. Review each platform's approach to see which aligns with your team's workflow.

Compliance features

Cliniko

Limitation: Marketing and patient recall features are limited, often requiring integration with Mailchimp or similar for targeted campaigns

Deputy

Fair Work compliance tools including break enforcement, maximum hour alerts, and award rate tracking reduce accidental non-compliance

Deputy highlights compliance features as a core strength. Cliniko offers the capability but does not position it as a primary differentiator.

Invoicing

Cliniko

Cliniko provides invoicing functionality, popular with Healthcare & Allied Health businesses

Deputy

Deputy provides invoicing functionality, popular with Hospitality & Tourism businesses

If invoicing is a daily-use area for your team, the onboarding curve and keyboard ergonomics matter more than feature counts - trial both with a real operator, not an evaluator.

Expense tracking

Cliniko

Cliniko provides expense tracking functionality, popular with Healthcare & Allied Health businesses

Deputy

Fair Work compliance tools including break enforcement, maximum hour alerts, and award rate tracking reduce accidental non-compliance

Deputy highlights expense tracking as a core strength. Cliniko offers the capability but does not position it as a primary differentiator.

Bank reconciliation

Cliniko

Cliniko provides bank reconciliation functionality, popular with Healthcare & Allied Health businesses

Deputy

Deputy provides bank reconciliation functionality, popular with Hospitality & Tourism businesses

For bank reconciliation, evaluate both platforms against your specific workflow requirements rather than feature lists alone. A free trial or vendor demo will clarify the differences.

Payroll

Cliniko

Cliniko provides payroll functionality, popular with Healthcare & Allied Health businesses

Deputy

Deputy provides payroll functionality, popular with Hospitality & Tourism businesses

Day-to-day payroll workflows feel different between Cliniko and Deputy - watch a recorded walkthrough of each before judging which fits your team.

Tax reporting and BAS

Cliniko

Letter and report templates with merge fields generate professional referral letters and clinical reports in seconds

Deputy

Limitation: Reporting is functional for scheduling and attendance, but lacks deeper workforce analytics without exporting data to a separate tool

If tax reporting and bas is a daily-use area for your team, the onboarding curve and keyboard ergonomics matter more than feature counts - trial both with a real operator, not an evaluator.

Multi-currency support

Cliniko

Cliniko offers multi-currency support capabilities. Support depth and SLA commitments vary by plan

Deputy

Deputy offers multi-currency support capabilities. Support depth and SLA commitments vary by plan

multi-currency support capabilities vary by plan tier on both platforms. Confirm the specific features you need are available at your target price point before committing.

Pricing Comparison

General pricing information for each platform.

Cliniko

Solo from approximately $55/month (1 practitioner), Team from approximately $109/month (2-5 practitioners), Growing from approximately $179/month (6-10 practitioners), Large from approximately $279/month (AUD). Annual billing discounts.

Pricing may vary based on team size, features, and region. Contact the vendor for the latest Australian pricing.

Deputy

Scheduling from approximately $4.50/user/month, Time & Attendance from approximately $4.50/user/month, Premium from approximately $6/user/month (AUD). Bundles available. Minimum spend may apply.

These figures are estimates based on publicly available pricing. Actual costs depend on your usage, team size, and any negotiated rates.

Pros & Cons

An honest look at the strengths and limitations of each platform.

Cliniko

Pros

Purpose-built for allied health with patient records, treatment notes, telehealth, and Medicare/DVA claiming built into the workflow
Online booking with practitioner availability, service selection, and intake forms reduces receptionist workload and fills empty appointment slots
Telehealth video consultations are included at no extra cost, allowing practitioners to offer remote consultations without a separate Zoom subscription
Letter and report templates with merge fields generate professional referral letters and clinical reports in seconds
Australian data hosting with encryption at rest and in transit meets Australian privacy and health records requirements

Cons

Per-practitioner pricing can be expensive for multi-disciplinary practices with many part-time practitioners
Inventory management for product sales (supplements, braces, etc.) is basic and requires workarounds or third-party tools
Marketing and patient recall features are limited, often requiring integration with Mailchimp or similar for targeted campaigns
Customisation of clinical templates requires understanding of Cliniko template syntax, which has a learning curve

Deputy

Pros

Drag-and-drop shift scheduling with templates and auto-scheduling saves hours of roster creation for multi-location businesses
Employee mobile app allows staff to clock in and out with GPS verification, swap shifts, and request leave without manager involvement
Fair Work compliance tools including break enforcement, maximum hour alerts, and award rate tracking reduce accidental non-compliance
Real-time labour cost tracking against budgets gives managers visibility into wage costs before the pay run, not after
Tasking module assigns and tracks tasks across locations, adding basic operational management beyond just scheduling

Cons

Per-user pricing adds up quickly for businesses with large casual workforces where many staff only work a few shifts per month
Advanced features like demand-based scheduling and auto-scheduling require Premium, doubling the per-user cost
Integration with accounting platforms like Xero and MYOB works well, but real-time sync can occasionally lag behind by several hours
Reporting is functional for scheduling and attendance, but lacks deeper workforce analytics without exporting data to a separate tool

Best For

Which tool suits which use case.

Choose Cliniko if you need

✓ Healthcare & Allied Health businesses
✓ Field service operations
✓ Moderate data needs (patients, appointments)
✓ Teams needing extensive third-party integrations
✓ Specialised compliance

Choose Deputy if you need

✓ Teams needing extensive third-party integrations
✓ Real-time data sync across platforms
✓ Financial reporting
✓ Hospitality & Tourism businesses
✓ Moderate data needs (employees, shifts)

Expert Verdict

Our Harvard-educated consultants' take on this comparison.

Clever Ops Recommendation

Cliniko and Deputy solve different problems: Cliniko handles industry tools, while Deputy covers accounting & finance. Most mid-market Australian businesses benefit from running both with a proper integration layer. Cliniko is the right pick when Australian allied health practices (physio, chiro, osteo, psychology, speech pathology) that need integrated patient management, online booking, and telehealth with Australian compliance built in. Deputy fits when shift-based businesses in hospitality, retail, and healthcare that need compliant scheduling, time tracking, and leave management with mobile accessibility for staff. Clever Ops can design the integration architecture and implement both, typically within 4-8 weeks.

Migration Notes

What to know about switching between Cliniko and Deputy.

Migrating Between Cliniko and Deputy

A successful migration from Cliniko to Deputy (or vice versa) is not just about data - it is about your team. Clever Ops handles the technical migration of your core data and custom fields, but we also provide hands-on training so your team is confident on the new platform from day one. The full process, including training, typically takes 4-8 weeks.

Cliniko vs Deputy FAQ

Cliniko may hit limits when medical practices needing GP-specific features (prescribing, pathology ordering) where Best Practice or Medical Director are more appropriate, or fitness businesses where Mindbody is better suited. Deputy may hit limits when salaried office-based teams where shift scheduling is irrelevant, or businesses with very large casual pools where per-user pricing becomes disproportionate to hours worked. Both platforms are designed to grow with your business, but scaling experience varies. Cliniko connects with 44+ tools, and Deputy with 47+, so integration flexibility at scale is comparable. Clever Ops helps mid-market Australian businesses plan their tech stack for growth, not just for today.

Yes. Cliniko provides a REST API and Deputy provides a REST + Webhook API, so automations can be built via Zapier, Make, or custom integrations. Common automated workflows include syncing shared data objects between both platforms. Clever Ops builds these automations for mid-market Australian businesses, saving teams 8+ hours/week on average.

Yes, both platforms are used by Australian businesses. Cliniko is popular with Healthcare & Allied Health in Australia. Deputy is widely used by Hospitality & Tourism and Retail & E-commerce. Key Australian considerations include AUD pricing, local support hours, GST handling, and data residency. Cliniko offers Australian-specific pricing. Clever Ops, based in Gippsland, Victoria, factors these nuances into every recommendation.

Full onboarding for either Cliniko or Deputy, including configuration, data import, and team training, typically takes 4-8 weeks with Clever Ops support. Self-service onboarding can take longer and often results in suboptimal configurations that limit the platform's value.

We audit your current workflows, team size, budget, and growth plans, then recommend the platform that fits. Our advice is vendor-neutral: we do not earn commissions from Cliniko, Deputy, or any vendor. Our Harvard-educated consultants have helped 50+ businesses make informed technology decisions over 12+. Book a free assessment to get started.

Cliniko: Solo from approximately $55/month (1 practitioner), Team from approximately $109/month (2-5 practitioners), Growing from approximately $179/month (6-10 practitioners), Large from approximately $279/month (AUD). Annual billing discounts.. Deputy: Scheduling from approximately $4.50/user/month, Time & Attendance from approximately $4.50/user/month, Premium from approximately $6/user/month (AUD). Bundles available. Minimum spend may apply.. When comparing costs, factor in per-user charges, add-on modules, and implementation costs, not just the headline price. Clever Ops can model the total cost of ownership for your team size during a free assessment.

Since Cliniko (industry tools) and Deputy (accounting & finance) serve different functions, many businesses run both. The key is connecting them so data flows automatically. Clever Ops builds these integrations, keeping your core records in sync across both platforms.

Both Cliniko and Deputy provide standard security measures including encryption, access controls, and compliance certifications. Cliniko uses a REST API and Deputy uses REST + Webhook, both supporting secure data transfer. For Australian businesses handling sensitive data under the Privacy Act, data residency and local support are worth verifying with each vendor. Clever Ops, based in Gippsland, Victoria, can review each platform's security posture against your compliance requirements during a free assessment.