Last updated 12 Oct 2026
Integrations
Invoices to QuickBooks Online, payments back
Send invoices and customers to your Australian QuickBooks company and see what's been paid.
Connect Autonomy Care to QuickBooks Online and your NDIS invoices and customers go to QuickBooks, with your tax codes, sales items and classes. Payment status comes back, so you can see what's been paid. It works with Australian QuickBooks companies. Payroll isn't included, because QuickBooks Online in Australia has no payroll connection.
What does the QuickBooks Online connection do?
It connects one Australian QuickBooks Online company to Autonomy Care.
Invoices
Sent invoices go to QuickBooks as invoices in Australian dollars, with a tax code and a sales item on every line. QuickBooks adds GST from each line's tax code.
The right customer
The plan manager for plan-managed supports, the participant if self-managed, or the NDIA if agency-managed. Each customer is found or created just before their first invoice.
Payments come back
Every 15 minutes Autonomy Care checks QuickBooks for payments and marks invoices paid, with the amount and date.
Cost centres as classes
Split income by SIL house, region or support category, using QuickBooks classes.
What goes to QuickBooks?
- Invoices, with GST shown separately, and the customer for each one.
- A voided invoice is voided in QuickBooks too.
What comes back?
Payment status, so you can see which invoices are paid.
When are invoices sent?
When you choose Push to QuickBooks on an invoice, or Sync now on the QuickBooks card in Settings, then Integrations, which sends every unsent invoice and then checks for payments. You can also turn on Send invoices automatically, which sends any unsent invoices every 15 minutes.
QuickBooks has no draft invoices, so only sent invoices go across.
How do tax codes and accounts work?
You choose the tax codes and the sales items to use; each item carries its income account. Cost centres go to QuickBooks classes.
How do we connect it?
Once, for your whole organisation. You need the Connect and manage integrations permission in Autonomy Care, and access to approve apps for your QuickBooks company.
Open Settings, then Integrations
In Autonomy Care, choose Connect QuickBooks on the QuickBooks card.
Sign in to Intuit and approve access
Sign in with your Intuit account, choose your company and approve access to its accounting data. Autonomy Care asks for accounting access only.
Check it's an Australian company
Autonomy Care only connects Australian QuickBooks companies, because the GST codes and NDIS invoicing assume one. A company from another country is refused and its access is removed straight away.
Check the suggested mappings
GST-free income, GST on income and a sales item are filled in for you. Anything Autonomy Care couldn't find is listed on the card as setup still needed.
Turn on class tracking for cost centres (optional)
To send cost centres, turn on class tracking in your QuickBooks company, then map each cost centre to a class.
Send a first invoice
Choose Push to QuickBooks on one invoice and check it in QuickBooks, then use Sync now for the rest.
What syncs, and when?
| What | Direction | When |
|---|---|---|
| Invoices (sent invoices only) | Autonomy Care to QuickBooks | Push to QuickBooks on an invoice, Sync now, or every 15 minutes with Send invoices automatically on |
| Customers: plan manager, participant or the NDIA | Autonomy Care to QuickBooks | Found or created just before their first invoice |
| Payment status, amount and date | QuickBooks to Autonomy Care | Every 15 minutes, and when you choose Sync now |
| Cost centres | Autonomy Care to QuickBooks, as classes | On every invoice line, when class tracking is on |
| Payroll and timesheets | Not sent | QuickBooks Online in Australia has no payroll connection. QuickBooks Payroll in Australia runs on Employment Hero, which Autonomy Care can connect to separately. |
Which tax codes does it use?
NDIS supports are usually GST-free. Autonomy Care maps GST-free income to your company's GST-free code and GST on income to your GST code. QuickBooks companies use either the simpler or the detailed set of GST codes, so check the suggestion matches the codes you use.
How do we pay staff if we use QuickBooks?
Use the payroll CSV export, or connect Employment Hero Payroll, which receives approved SCHADS hours as timesheets. QuickBooks Payroll in Australia runs on Employment Hero.
What if something fails?
Every send is logged. Rate limits and outages are retried automatically; a missing mapping waits for you to fix it and press Retry.
Each record is sent once: Autonomy Care remembers what it sent, so a retry never makes a duplicate invoice.
Troubleshooting
| What you see | Why | What to do |
|---|---|---|
| Needs reconnecting on the QuickBooks card | QuickBooks stopped accepting the connection, for example because the app was disconnected in QuickBooks | Choose Reconnect QuickBooks. Your mappings and links are kept. |
| The company was refused | It isn't an Australian QuickBooks company | Connect your Australian company instead. |
| An invoice is waiting for a mapping | A tax code, sales item or class has no match yet | Map it in Settings, then Integrations, then QuickBooks, then press Retry in the Sync log. |
| There are no invoices to push | QuickBooks only accepts sent invoices, not drafts | Send the invoice in Autonomy Care first. |
| QuickBooks rejected an invoice | QuickBooks' own reason is shown in the Sync log | Fix the cause, then press Retry. |
What it does and doesn't do
It does
- Sends invoices and customers
- Brings payment status back
- Voids invoices you void
- Logs every send, with Retry
It doesn't
- Doesn't send payroll or timesheets
- Doesn't connect companies outside Australia
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See it with your own invoices
Book a demo and we'll show the QuickBooks connection with your questions.