This guide explains how to set up Deputy for a healthcare business. Deputy brings scheduling, attendance, payroll, communication, and reporting together in one place. It covers how to structure Locations and Areas, manage team access, prepare payroll workflows, review scheduling and attendance settings, and plan your rollout.

Before you read

Target audience: This article is for users with System Administrator access.
Free trial: If you haven't signed up for Deputy yet, see Creating an Organization and Getting Started with a Free Trial. When signing up, select the industry that best matches your business.
Returning to your trial: If you've already signed up, log in at once.deputy.com to continue setting up your account.
Watch Deputy in Action: Before you start, watch Deputy in Action to see how Deputy works and what you'll be setting up throughout this guide.

This article covers:

Choose your organisational structure
Review Location settings before rollout
Set access and approval responsibilities
Prepare payroll and Smart Scheduling workflows
- Smart Scheduling, analytics, and labour insights
Run day-to-day healthcare workflows
Quick add-on and plan check
Five-step onboarding checklist
Avoid common healthcare set-up mistakes
Get more help

Choose your organisational structure

In Deputy, Locations usually represent clinics, practices, healthcare sites, departments, regions, or mobile teams. Areas represent the departments, roles, service types, treatment spaces, or coverage groups where team members perform their work.

Choose a starting model that reflects how your business manages schedules, reporting, payroll export codes, permissions, and site or department access. You can refine the structure as your use of Deputy grows.

Business type	Suggested starting structure	Healthcare Area examples	Things to consider
Single clinic or practice Medical, allied health, dental, imaging, and specialist practices	One Location representing the clinic or practice	Reception, Nurses, Clinicians, Admin, Treatment Room, and Imaging	This structure keeps site-level scheduling, approvals, attendance, and reporting together.
Multi-site healthcare group Healthcare groups operating across multiple clinics or sites	One Location for each physical clinic or site	Reception, Nurses, Clinicians, Admin, Imaging, and service types	Site managers can manage local schedules and approvals. Shared staff need access to each relevant Location.
Healthcare business requiring department separation Larger clinics, imaging providers, day hospitals, and multi-department groups	Separate Locations for departments requiring stronger access boundaries	Shift types, seniority, service types, or coverage groups	Consider this when department managers need separate approvals, schedule management, reporting, or wage visibility boundaries. Too much separation can make whole-site visibility harder.
Mobile or community healthcare Community health, home visits, outreach, and mobile healthcare teams	A region as the Location	Home Visits, Community Clinic, Admin, service types, and Travel	Mobile clock-in and GPS capture can support changing work locations. Keep clinical visit management in the appropriate specialist system.

When you plan your structure, consider:

Shared team members: Team members who work across multiple clinics, sites, or departments need access to each relevant Location.
Permission boundaries: Areas can support coverage and reporting, but separate Locations may be needed when managers require stronger access, approval, or wage visibility boundaries.
Reporting and export codes: Consistent Area names and export codes can support payroll, finance, department, role, and site reporting workflows.
Other healthcare systems: Deputy is usually used alongside clinical records, patient booking, billing, patient communication, practice management, and clinical compliance systems. Keep those specialist workflows in the appropriate healthcare system where they already sit outside Deputy.

For a complete overview, see Organisations, Locations and Areas.

Review Location settings before rollout

Location settings control many of the defaults used for scheduling, clock-in, timesheets, approvals, and reporting. Review the settings that apply to your workflow before your team starts using Deputy.

Review the physical address and map pin: Accurate Location details support clock-in settings for fixed clinics and can support mobile attendance workflows where GPS capture is used.
Set up Training Tags: Training Tags can identify team members who are qualified, trained, or approved to work in particular Areas. Common healthcare examples include First Aid, CPR, Working with Children, Infection Control, Medication Administration, Radiation Licence, Clinical Qualification, and Practice Induction.
Review Shift Locking: Shift Locking can limit changes to scheduled shifts after a configured time.
Review Timesheet Auto-Approval: Manual approval during an initial rollout allows managers to review overtime, breaks, late finishes, and attendance exceptions before payroll.

For a complete overview of every Location setting, including General, Areas, Scheduling, and Timesheet settings, see Creating your Locations.

Set access and approval responsibilities

Access levels control who can manage schedules, approve timesheets, view wage information, and change account settings.

Deputy access level	Common healthcare users	Common responsibilities
System Administrator	Owners and operations leaders	Manage account structure, integrations, access, and account-wide settings.
Location Manager	Practice, clinic, and operations managers	Manage schedules, labour budgets, wage visibility, approvals, and site reporting.
Supervisor	Department leads and team supervisors	Manage daily attendance, breaks, and timesheet exceptions without access to wage or schedule cost information.
Employees	Reception, nurses, clinicians, practitioners, and admin teams	View schedules, clock in and out, request leave, and review team updates.

For a complete overview, see Deputy access levels and permissions.

Once you've set access levels, add your team members and assign them to the Locations where they work. You can add team members individually, add multiple team members, import them from another system, or invite them to join Deputy.

For a complete overview, see Adding team members.

Prepare payroll and Smart Scheduling workflows

Healthcare payroll can include overtime, weekend work, public holidays, call-outs, allowances, higher duties, salaried practitioners, part-time contracted hours, and leave. Pay Templates and Pay Rate Builder can support your pay conditions, while Leave Policies control the types of leave available to team members and how leave is managed in Deputy.

You can process payroll using Deputy Payroll where available, or connect Deputy to a supported third-party payroll provider.

Click to expand for each payroll option.

Deputy Payroll (AU)

Deputy Payroll (AU) is Deputy’s integrated payroll option for Australian businesses. It keeps scheduling, attendance, approved timesheets, and payroll within Deputy, so you can move from worked hours to a pay run without exporting timesheets to a separate payroll provider.

Set-up includes your business and payroll details, pay calendars, superannuation, deductions, extra earnings, and team member payroll information.

For a complete overview of setting up and using Deputy Payroll (AU), see Getting started with Payroll (AU).

Deputy Payroll enabled by Paycor (US)

Deputy Payroll enabled by Paycor (US) connects Deputy workforce management with Paycor payroll. Deputy manages scheduling, time tracking, leave, pay rates, and approved timesheets, while Paycor can be used to handle payroll functions such as tax filings, banking, and year-end processing.

Approved timesheets can be exported directly from Deputy to Paycor, reducing the need to manually re-enter worked hours.

For a complete overview of how Deputy and Paycor work together, see Getting started with Deputy Payroll enabled by Paycor (US).

Third-party payroll integration

If you already use another payroll provider, you can keep Deputy focused on scheduling, attendance, timesheets, and pay calculations, then send approved timesheet data to your existing payroll system. Deputy supports payroll integrations including Xero, MYOB, QuickBooks, ADP, and other providers, with the exact workflow and data available depending on the integration you use.

For healthcare businesses, review how Locations, Areas, roles, export codes, allowances, and timesheet information need to flow between Deputy and your payroll, accounting, HR, finance, or practice management systems.

For a complete overview of the available payroll connections, see Payroll integrations.

For more information on Leave management, see:

Keep payroll testing simple

Run a test export before your first live pay run. Focus on:

Regular hours: Confirm that standard hours and pay rates appear as expected.
Overtime: Confirm that overtime hours and rates appear as expected.
Healthcare pay conditions: Test relevant conditions such as weekends, public holidays, higher duties, allowances, or call-outs where they apply to your workforce.

Smart Scheduling, analytics, and labour insights

You can compare schedule costs with labour budgets, sales data, or other workforce information while building schedules. Business Insights cost panel can help you review labour cost information alongside other analytics and reporting views.

Common reports include:

Schedule, timesheet and sales comparison: Compare scheduled and actual hours and wage costs, review cost variance, and track labour percentage against sales.
Attendance & absence: Review no-shows, late arrivals, and early departures by Location, Area, or team member to see where attendance is affecting scheduled coverage.
Schedule adherence by team member: Compare scheduled hours with actual hours worked and identify the cost variance when team members work outside the original schedule. (Requires Analytics+)

Clinic, department, and workforce reporting

If labour reporting by clinic, department, site, or role matters, use Areas, Area export codes, and consistent naming conventions. This can support cleaner payroll exports and workforce reporting across clinical, admin, and support teams.

Healthcare businesses may review workforce activity by:

Clinic or site
Department
Role
Scheduled versus actual hours
Overtime
Missed breaks
Attendance exceptions
Shared staff across sites

Shared staff are particularly important to test where employees work across multiple clinics or departments. Review Location access, scheduling, approvals, and reporting before wider rollout.

Click for a complete overview of Smart Scheduling, workforce reporting via Deputy Analytics, and business insights.

Run day-to-day healthcare workflows

Clocking in: Kiosk or mobile app

Choose the clock-in method that matches where your team works.

Kiosk: A shared tablet Kiosk can support fixed clinics, practices, and healthcare sites and can use PIN access and photo capture where enabled.
Mobile app: Mobile clock-in can support community and mobile healthcare teams working away from a fixed clinic or practice.

GPS capture can support attendance review for mobile teams. Strict location controls may not suit practitioners travelling between homes, community sites, clinics, or changing addresses, so review your clock-in configuration against how your mobile teams actually work.

For a complete overview of the available clock-in methods, see Using Deputy across different devices.

Manage schedule adjustments

Healthcare schedules may need coverage across reception, nurses, clinicians, treatment rooms, imaging, admin, and support roles. Areas can help managers review coverage before schedules are published.

Open shifts let eligible team members apply for available shifts. Shift swaps let team members request changes to assigned shifts.

Manager review can help confirm that a team member has the required qualifications, training, availability, Location access, and approval before a schedule change is accepted.

Click to learn more about open shifts, shift offers, and shift swaps.

Communicate with your team

News Feed and Messaging can be used to share schedule changes, urgent coverage needs, practice announcements, policy reminders, site updates, and team announcements.

Messaging+ includes additional messaging features, such as larger groups, more message history, read receipts, and role-based conversations. This can support communication groups for clinics, departments, practitioners, admin teams, or mobile healthcare teams.

Click to learn more about the News Feed and Deputy Messaging.

Quick add-on and plan check

The following add-ons and plan options may be useful as your use of Deputy grows. To check what is included in each plan or add-on, see our pricing plans.

If you need to...	Review this feature	Common use case
Send onboarding forms, store employee documents, and track licences, qualifications, certifications, or training expiry dates	Deputy HR	Businesses that need employee records, onboarding documents, qualifications, policy acknowledgements, or compliance records connected to workforce operations
Create custom reports, schedule emailed reports, and review overtime, attendance, department, site, or staffing trends	Analytics+	Managers or operators who need deeper workforce reporting across clinics, departments, roles, and sites
Set up custom roles, additional Location hierarchy, and more detailed permission controls	Deputy Pro	Businesses with more complex site, department, shared-team, access, or reporting requirements

Five-step onboarding checklist

These stages apply whether you are evaluating Deputy, testing it with a smaller group, or rolling it out across your full business.

Set up your structure: Create your Locations and Areas, choose naming conventions, and review any required export codes.
Add your team and schedules: Add team members, assign access levels, set up pay details, and create your first schedule.
Test your workflows: Test clock-in, breaks, leave requests, schedule changes, qualification requirements, and notifications with a pilot group.
Review timesheets and payroll: Approve pilot timesheets and test regular hours, overtime, breaks, public holidays, relevant pay conditions, and payroll output.
Go live: Train managers, publish the live schedule, and roll Deputy out to the rest of your team.

For a guided onboarding checklist, open the Help menu by selecting the ? icon in your Deputy account, then select Start here.

Avoid common healthcare set-up mistakes

Common mistake	Why it causes problems
Giving every department lead wage visibility	Exposes wage information when Supervisor access may be enough for daily department management. Review Deputy access levels to choose the appropriate level of access.
Making every department a Location too early	Can fragment whole-clinic visibility and make schedule management harder. Use separate Locations when stronger permission, approval, reporting, or wage visibility boundaries are required.
Not testing shared staff workflows	Can create scheduling, Location access, approval, and payroll issues when team members work across multiple clinics or departments.
Not using Training Tags for qualification-sensitive work	Can result in team members being scheduled into Areas where they do not have the required qualification, training, induction, or approval.
Allowing schedule changes without manager review	Can create coverage or qualification issues when open shifts, shift offers, or swaps are accepted without appropriate review.
Using strict location controls for mobile healthcare teams	Can create clock-in problems when practitioners move between homes, community sites, clinics, or changing addresses.
Skipping a payroll test export	Can leave pay rate, overtime, allowance, higher-duty, break, or export issues undiscovered before the first live pay run. Learn how to export timesheets from Deputy and test your payroll workflow before going live.

Get more help

During your trial, use the Action Bar to access setup help without leaving Deputy.

From the Action Bar, you can:

Select Start here to open Deputy Essentials, where you'll find bite-sized videos and guided walkthroughs to help you set up your business at your own pace.
Select Ask an expert to connect with an SMB Consultant.
Select the ? icon to open the Help menu and access support options.

You can collapse the Action Bar or drag it to another position on the screen.

Help Centre

For help and support, see Get help and request support from Deputy.