Getting Started with ClinicFlow

A step-by-step guide to setting up and running your first payroll

1. Create Account
2. Configure Settings
3. Export CSV
4. Generate Payroll
5. Review Workbook
6. Send Invoices
7. Track Approvals
faq. FAQ
Step 1 Create Your Account
  1. Go to the ClinicFlow home page and click Get Started or Start Free Trial.
  2. Enter your name, email address, and choose a password (minimum 8 characters).
  3. Pilot / invite code — if you received a pilot code from iMentalHealth, enter it in the Invite Code field. This gives you a 2-month free trial with full access.
  4. Click Create Account. You'll land on Settings to complete your setup.
No credit card is required to create an account. Pilot users get 60 days free. After your trial, subscribe on the Pricing page.
Subscription options
  • Monthly — $59 CAD/month
  • Annual — $549 CAD/year (save $159)
  • Up to 30 contractors, unlimited payroll runs
Step 2 Configure Your Settings

Settings are shared across every payroll run. Fill these in once — ClinicFlow will pre-fill every workbook for you.

A. Clinic Identity
  • Clinic Name — appears on all invoices
  • Address — full mailing address
  • GST / HST Number — e.g. 123456789 RT0001
  • Fiscal Year — e.g. 2026
B. Contractor Rate Card

Up to 30 contractors. For each one:

  • Name + Email — used for invoice delivery
  • GST # — contractor's business number
  • T1 Rate — therapy payout % for sessions 1–threshold (e.g. 60 for 60%)
  • Threshold — session count where T2 rate kicks in
  • T2 Rate — payout % after threshold
  • Report / Court / VAC / Supervision — payout % per service type
Enter rates as whole numbers: 60 means 60%, not 0.60.
C. Service Type Mappings

Maps each service name from your CSV to a ClinicFlow billing category. Common names are pre-loaded. Add any custom service names from your platform.

Default categories:
  • Therapy
  • Report / Assessment
  • Court Report
  • VAC Therapy
  • VAC Assessment
  • Supervision
  • No Charge
Complete Settings before generating any payroll. Contractor names and rates are embedded in the downloaded workbook — changes in Settings only apply to future runs.
Step 3 Export Your CSV Report
Export from your platform:
  • Jane App Reports → Sales by Staff Member → set date range → Download CSV
  • Owl Practice Reports → Invoices / Sessions → Export CSV
  • Cliniko Reports → Invoices or Appointments → Export CSV
  • Any other platform Export any CSV with client, practitioner, service, and amount columns. Use the Universal CSV Importer to map custom columns.
Tip: Drag and drop the .csv file directly onto the Payroll page, or open it in a text editor, select all (Ctrl+A), copy, and paste into the portal.
Auto-detected columns

ClinicFlow recognises these columns (and common aliases from any platform):

Patient / Client / Customer
Staff Member / Practitioner / Provider
Item / Service / Description
Invoice # / Invoice Number
Purchase Date / Service Date / Date
Subtotal / Fee / Net
Collected / Amount Paid / Paid
Balance / Outstanding
Payer / Insurance / Fund
Total / Amount
Don't see your column names? Use the Universal CSV Importer to save a custom mapping for your platform.
Step 4 Generate Your Payroll Workbook
  1. Click Generate Payroll in the top navigation.
  2. Select the Payroll Month from the dropdown (e.g., March).
  3. Confirm or adjust the Fiscal Year.
  4. Paste your copied Jane CSV data into the text area.
  5. Click Generate Workbook & Download.
  6. Your browser will download a file named ClinicFlow_[ClinicName]_[Month].xlsx.
No CSV yet? Leave the text area blank and click Generate. You'll get a fully structured workbook with all your clinic settings pre-filled — you can paste data manually into the Raw Data tab in Excel.
You can generate the workbook multiple times for the same month — each run creates a fresh, clean file. Previous runs are logged in your Dashboard.
Step 5 Review Your Workbook

Your downloaded Excel file contains 10 tabs. Here's what each one does:

Tab Purpose What to do
Cover / Instructions Overview of the workbook, contact info, and tab guide. Read only
⚙ Settings Clinic details, contractor rate card, and service type mapping — pre-filled from your portal settings. Review; yellow cells are editable
📋 Raw Data Every session row from your CSV import, with date, patient, item, payer, and amounts — parsed by ClinicFlow. Review; add/remove rows if needed
🚦 Payment Status Auto-flags each invoice as Paid, Partial, or Unpaid based on Balance column. Review only — formula-driven
📊 Contractor Summary Per-contractor payroll: T1/T2 therapy, reports, court, VAC, supervision — all calculated by ClinicFlow from your session data. Review; ClinicFlow does the math
🧾 Invoices Printable invoice for each contractor showing session counts, gross, rate, and payout. Print or save; invoice #s editable
🏦 Clinic Revenue Total gross revenue by payer (Blue Cross, Medavie, WCB, VAC, Private) and by service type. Review monthly revenue breakdown
📈 P&L Dashboard 12-month P&L: gross revenue, contractor payouts, net. Auto-fills current month. Archive each month with Paste Special → Values
⚠ Unpaid Clients List of all client invoices with outstanding balances for follow-up. Follow up on collections
📬 Invoice Status Tracks which contractors have been emailed and whether they have approved. Updated by the portal when you send invoices
Yellow cells are editable input fields — everything else is formula-driven. Do not paste values over formula cells or the workbook calculations will break. To archive a month's P&L data: copy the row → Paste Special → Values Only.
Step 6 Send PDF Invoices to Contractors
  1. Click Invoices in the top navigation.
  2. Find your payroll run in the list and click Send Invoices.
  3. ClinicFlow generates a PDF invoice for each contractor and emails it automatically.
  4. Each email includes:
    • The contractor's PDF invoice as an attachment
    • A unique one-click approval link
    • Clinic name, invoice number, and payroll month
Invoices are sent to the email addresses entered in Settings → Contractor Rate Card. Double-check contractor emails before sending.
What the contractor receives
  • An email from your clinic's address
  • Subject: "[ClinicName] Invoice — [Month] [Year]"
  • PDF attachment with session breakdown and payout amount
  • A button: "Review & Approve Invoice"
Step 7 Track Contractor Approvals
For the contractor:
  1. They receive the invoice email.
  2. They click the Review & Approve Invoice link.
  3. They review their invoice in the browser.
  4. They click Approve — done.
For the clinic admin (you):
  • Go to Invoices in the portal.
  • See each contractor's status: Sent, Approved, or Not Sent.
  • The Invoice Status tab in your Excel workbook also reflects these statuses.
  • No chasing contractors by email for signatures.
Managing Your Subscription

After your trial period, subscribe on the Pricing page. You can update your payment method, download receipts, or cancel anytime via the Billing link in the top navigation (powered by Stripe — no card details are stored by ClinicFlow).

TROUBLESHOOTING
My contractor payouts are $0 — what happened?

Check that the Staff Member names in your Jane CSV exactly match the contractor names in Settings. ClinicFlow matches on name — even a trailing space or different capitalisation will cause a mismatch. Copy the name directly from Jane.

A service type is showing as Uncategorised.

Go to Settings → Service Type Mappings and add the Jane service name exactly as it appears in your CSV (copy-paste from the Item column to be safe). Assign it to the correct category and save.

The workbook downloaded but some numbers look wrong.

Re-check your Settings: confirm Tier 1 % and threshold are correct for each contractor, and that the fiscal year matches. Regenerate the workbook after saving any changes.

Contractors are not receiving invoice emails.

Confirm contractor email addresses are correct in Settings. Check your spam folder. If you are testing locally, SMTP must be configured in your .env file. Contact support if the issue persists.

I need more than 30 contractors.

Contact us at admin@imentalhealth.ca — we can accommodate even larger clinics.

Which practice management platforms does ClinicFlow support?

ClinicFlow works with CSV exports from Jane, Owl, Cliniko, and any platform that exports session or invoice data. It auto-detects column headers, so no manual mapping is needed for common platforms. For unusual column names, use the Universal CSV Importer to define your own mapping and save it as a template.

FREQUENTLY ASKED QUESTIONS
General

ClinicFlow automates contractor payroll and invoicing for health and psychology clinics. You export your monthly session data from your scheduling software as a CSV, paste it into ClinicFlow, and it calculates what each contractor is owed, generates an Excel workbook, and emails each contractor a PDF invoice with a one-click approval link. It is not accounting software — think of it as the step between your scheduling platform and your accountant.

No. ClinicFlow is a payroll automation and contractor invoicing tool. It does not do double-entry bookkeeping, bank reconciliation, tax filing, or a full chart of accounts. For full accounting you still need software like QuickBooks, Wave, or Xero. ClinicFlow handles the payroll side; your accountant handles the rest.

Yes — ClinicFlow now supports CSV exports from Jane, Owl, Cliniko, and any platform that includes session or invoice data. Column headers are detected automatically. For platforms with unusual column names, use the Universal CSV Importer (/payroll/upload) to define a custom mapping and save it as a reusable template.

No. ClinicFlow is an independent product built by iMentalHealth Counselling. It is compatible with Jane's CSV export format but is not affiliated with, partnered with, or endorsed by Jane App.
Payroll & Workbook

No. The workbook is a payroll document — it captures contractor sessions and payouts from your CSV export. Operating expenses (rent, software, supplies, etc.) are tracked separately in the Finances page and do not affect the workbook. Enter them there at any time during the month.

Once per payroll period — typically at month end after all sessions for that period are finalised. You can regenerate the workbook as many times as you need; each run creates a fresh file. Previous runs are listed on your Dashboard so you can re-download them any time.

Go to the Dashboard and delete the incorrect payroll run using the trash icon. This removes the run record and any invoices sent for it. Then re-run for the correct month.

This almost always means the Staff Member (or Practitioner/Provider) name in the CSV does not exactly match the contractor name in Settings. Even a small difference in spelling, spacing, or capitalisation will cause a mismatch. Copy the name directly from a CSV row and paste it into Settings to be sure.

Yes. Leave the CSV area blank and click Generate. You'll get a fully structured workbook with your clinic settings pre-filled — you can paste data manually into the Raw Data tab in Excel, or use it as a template.
Invoices & Approvals

They get an email with a PDF attachment showing their session breakdown, payout amount, and billing period. The email also contains a button to open their approval page in a browser, where they can review the invoice and optionally submit any expense reimbursement requests before approving.

Yes. As soon as a contractor clicks Approve, ClinicFlow sends you an email notification with their name, payroll month, invoice amount, and a table of any expenses they submitted for reimbursement.

Yes. When a contractor opens their approval link, they see a form to add any work-related expenses before approving — such as professional memberships, office supplies, or other business costs. You receive these in the approval notification email and can decide whether to include them in the payout. Submitted expenses are also visible in the Invoices page under each contractor's row.

Have them contact you directly. You can delete their invoice record in the Invoices page (their approval link will stop working) and resend a corrected invoice once the issue is resolved.

Yes. In the Invoices page, each contractor row has a Resend button that emails a fresh PDF invoice and a new approval link to that contractor only.
Outstanding Payments

ClinicFlow tracks outstanding balances per session. When you upload an updated CSV the following month, it will pick up any payments that came in and include the catch-up amounts in that month's payout. The outstanding sessions are also listed in the Invoices page so you can follow up with clients.

Yes — as long as the session appears in your Jane CSV with an updated collected/balance figure, ClinicFlow will reflect the new payment in the next payroll run. You do not need to manually track or enter catch-up payments.
Privacy & Data

ClinicFlow stores only the minimum needed for payroll calculations. Patient names from your CSV are stored as initials only (e.g. "J.S.") — never as full names. Session amounts, dates, and service types are stored so they can appear on contractor invoices, but no clinical notes or health records are ever collected or stored.

Only authenticated users belonging to your clinic can access your payroll data and invoices. Contractors can only view their own invoice via their unique approval link — they cannot see any other contractor's information.
Billing & Subscription

You get 14 days free with full access to all features. Clinics that receive a pilot invite code from iMentalHealth get 60 days. No credit card is required to start. After the trial you can subscribe monthly ($59 CAD/month) or annually ($549 CAD/year).

Yes. Click Billing in the top navigation to open the Stripe customer portal, where you can cancel, change your plan, or update your payment method. If you cancel, you keep access until the end of your current billing period.

No. All payment processing is handled by Stripe. ClinicFlow never sees or stores your card number.
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