🖥️ For practice admins using Practice HQ on the web. Everything in payroll needs the Payroll permission, which is separate from Billing.
This article explains how to set up and run payroll in Practice HQ: who can use it, pay periods and provider pay, what counts toward payroll, payment-readiness rules, adjustments, marking pay as paid, and exports. Oasys calculates what each provider is owed from money your practice has actually collected, and you make the actual payment outside Oasys and mark it paid here.
In this article
1. Who can use payroll
This section explains where payroll lives and who can open it. Find it under Payroll in the Administration section of the Practice HQ sidebar.
Payroll has its own Payroll permission, separate from Billing. In Permissions, it's listed under Operations: "View and export payroll, manage compensation settings, provider overrides, periods and adjustments, and mark payroll as paid."
Only the owner role has Payroll by default. Admins, billers and other roles need it granted.
Without the permission, Payroll doesn't appear in your Practice HQ sidebar.
The Payroll tab appears only when payroll is turned on for your practice and at least one billing feature (practice billing or practice insurance) is on.
Payroll isn't available for practices set up in Charter School mode.
Providers don't have a payroll view of their own.
2. Setting up payroll
This section covers the pay-period and pay-split settings. Open Payroll → Payroll settings, then set the following under Pay periods.
Frequency: Weekly, Every two weeks, or Monthly.
First cadence period: the date pay periods are calculated forward from.
Timezone: used for period boundaries. Choose Eastern (ET), Central (CT), Mountain (MT), Arizona (MST), Pacific (PT) or UTC.
Practice share: the percentage of collected revenue, after processing fees, that the practice keeps. The rest is the provider's pay.
Practice share can use up to two decimal places (for example 35.25%), from 0% up to, but not including, 100%.
Pay is a percentage split only. There are no fixed per-session rates and no rates by service type or CPT code.
⚠️ Important: A change to Frequency or First cadence period must start within or after the current pay period, never before it. If the current period already has payable items, start the change on that period's first day or after the period ends. Oasys also won't save a change that would start before the end of your last paid payroll period.
3. Custom pay periods
This section is for practices whose payroll calendar doesn't follow a fixed weekly, every-two-weeks or monthly cadence.
There's no built-in semi-monthly frequency. A custom pay-period mode is available for practices that need periods like the 15th and the last day of each month.
Custom mode is a one-way switch. Once you move to custom periods, you define each period's start and end dates yourself, and there's no switch back to a standard cadence.
To turn on custom mode, contact Oasys support.
Managing custom periods
Open Payroll → Payroll settings and go to Custom pay periods.
Under Add a period, enter the Period start and Period end, then click Create. The end date must be on or after the start date.
Check for a Dates need a payroll period warning. It lists current or past dates no period covers, so payroll can't include them until you add or edit a period.
To remove a period, delete it from the list and confirm with Delete period.
Once a period has paid items, its dates can't be changed and the period shows as Locked.
4. What counts toward payroll
This section explains which money lands in a pay period. Payroll counts money your practice has actually received, not what was billed.
Which payments count
An item lands in the pay period of the date it was paid (in your payroll timezone), not the date of the session.
Money that counts: paid client invoices (net of any refunds), standalone invoices, insurance claims that came back paid or partially paid, client-responsibility invoices, and external payments you recorded.
Sessions paid with client credits show as Credits applied. A client's share marked as paid outside Oasys shows as External PR Payment.
Completed sessions, no-shows and late cancellations can count once they're paid. A cancelled session counts only if a paid invoice is attached to it.
Group sessions count once per attendee.
A session billed with additional services (add-on CPT lines) counts with all of its paid lines.
If a session was billed again after a failed or voided invoice, only the invoice that carries the money counts, so it isn't paid twice.
Refunds, takebacks and fees
If an insurance payment arrives dated inside a period you'd already marked paid for that provider (for example, you marked them paid before the period ended), it's carried into their next unpaid period instead of changing the paid one.
Fully refunded invoices drop out. Partial refunds are netted off.
If a payer takes money back on a claim, or a client invoice is refunded because of a takeback, Oasys adds a negative adjustment to the provider's latest unpaid period automatically.
Card-processing and platform fees on card payments are subtracted before the practice share is applied. Insurance payments and external payments carry no fees in payroll.
Insurance claim processing fees aren't part of payroll. They're billed to your practice separately.
The calculation is: Collected minus Fees gives the net received. The Practice Share percentage of that goes to the practice. The rest, plus any adjustments, is the provider's Net Pay.
5. Payment readiness (documentation rules)
This section covers what must be done before a session is ready to pay. Open Payroll settings → Payment Readiness and choose from:
Session notes: the session has a note.
Therapist signature: the note is signed.
Supervisor approval: supervised sessions must be approved by a supervisor. This option appears only if your practice uses supervision.
No-shows and cancellations don't need documentation. Client-responsibility invoices need notes only. Then choose When documentation is incomplete:
Show a warning but allow payment: items are flagged Needs review, but you can still mark the provider paid.
Prevent payment until resolved: Mark as paid is greyed out for that provider until every item is ready.
Either way, incomplete items still count in the period's totals. The setting controls whether you can mark the provider paid, not what's calculated. By default, Session notes is on, the other two are off, and warning mode is selected.
6. Viewing pay periods
This section explains how to read a pay period. Use the period dropdown at the top of Payroll to switch periods.
Periods are tagged Current, Upcoming or Past.
The list shows your eight most recent periods, so older periods may not be available here. Use your exports for historical records.
Summary cards
Payable items: how many entries are in the period, and how many providers have payable activity.
Net payroll: total net pay, with Collected and Fees underneath.
Paid therapists: how many providers are marked paid, and how many are awaiting payment.
Compliance: how many items are ready, and the percentage ready.
Provider table and details
The table lists each provider with Compliance, Collected, Fees, Practice Share, Adjustments, Net Pay and Status (Paid, Ready or Needs review).
Open a provider's ⋮ menu → View details to see every entry: client, session status, service date, Date Paid, documentation status (and what's missing: notes, signature or approval), amount charged, and provider pay.
In View details, Note opens the session note read-only.
7. Per-provider practice share
This section shows how to give one provider a different split. Open Payroll settings → Individual Practice Share.
Enter a different practice share percentage for any provider.
Leave a provider's box empty to use the practice-wide Practice share.
A provider's own percentage always takes priority over the practice default.
8. Adjustments
This section covers bonuses, deductions and corrections. Open a provider's ⋮ menu → Add adjustment.
Enter an Amount ($). Positive amounts increase pay (bonuses, corrections). Negative amounts reduce it (deductions).
Enter a Reason. It's required, up to 500 characters.
Click Save adjustment.
The amount can't be zero or larger than $99,999.99.
Adjustments change that provider's Net Pay for the period.
Adjustments can't be edited. To fix one, remove it from View details and add a new one.
Once a provider is marked paid, their adjustments for that period can't be changed.
9. Marking pay as paid
This section shows how to record that you've paid a provider for a period outside Oasys.
Find the provider in the period's table.
Open the ⋮ menu and click Mark as paid.
Confirm. The dialog tells you this locks the provider's pay at the shown net amount for the period.
You mark each provider paid individually. There's no single "pay the whole period" button.
Oasys records who marked it paid and when, and saves the provider's pay for that period as it stood at that moment.
After a provider is marked paid, their items show as Settled, whatever their earlier documentation status.
On custom pay periods, marking a provider paid also locks that period's dates.
⚠️ Important: Marking pay as paid can't be undone by the practice. There's no unmark, undo or reverse control anywhere in payroll. Confirm the period and amounts are right before you mark it paid. If you marked pay as paid by mistake, contact Oasys support.
10. Exporting payroll
This section covers exports for your records or your own payroll process. Open Payroll → Export → Export as Excel or Export as PDF.
An export always covers the whole selected period for all providers. There's no single-provider export.
It includes a summary (providers, payable items, total collected, processing fees, net payroll, adjustments, paid providers), a per-provider summary, the detailed entries, and the adjustments.
The details section includes client names. Treat the file as confidential.
💡 Tip: Oasys payroll is a tracking and calculation tool. It doesn't integrate with external payroll providers. You handle actual payments outside the platform and mark them as paid here.
Frequently asked questions
Does payroll integrate with Gusto, ADP, Paychex or QuickBooks?
No. Oasys calculates payroll and lets you export it as a PDF or Excel file. You run the actual payment outside Oasys and then mark it paid here.
I marked a provider paid by mistake. What should I do?
There's no self-serve reversal. Contact Oasys support.
Can I set different percentages for different providers?
Yes. Use Individual Practice Share in Payroll settings to set a provider's own percentage, which takes priority over the practice default.
What happens if a session isn't compliant?
It's still counted in the totals and marked Needs review. With Show a warning but allow payment you can still mark the provider paid. With Prevent payment until resolved you can't until it's fixed.
Why isn't a session I just held showing up in payroll?
Payroll only counts money that's been collected. A session appears in the period its payment arrived in, so an unpaid invoice or an unpaid claim isn't on payroll yet.
Why can't I see the Payroll tab?
You need the Payroll permission (Billing alone isn't enough). Ask your practice owner to grant it in Permissions.
Why was my pay-schedule change rejected?
A new frequency or start date can't begin before the current pay period or inside a period that's already been paid. If the current period already has payable items, it must start on that period's first day or after it ends. Choose a later start date.
Where do I set up Stripe, fix an invoice, or undo a waived or paid charge?
Those are billing tasks, not payroll. See Billing sessions, invoices and payments.