Integrations

Connecting QuickBooks Online: certified valuations as sales invoices

3 min read · Checked against the product 3 October 2026

Connect QuickBooks Online and every certified valuation becomes a sales invoice, with the retention and the VAT treatment set for you, and a payment in QuickBooks marks the valuation paid. For UK organisations on the paid plans.

For UK organisations on Builder, VariationFlow and VariationFlow + QA Flow, and on older paid plans; not on the free plan. An admin or director connects it, and one accounts package can be connected at a time.

What it does

With QuickBooks connected, the certificate you record in VariationFlow becomes the sales invoice in your accounts, and when QuickBooks shows the invoice paid, the valuation follows. An interim application is not a sales invoice, so nothing goes to QuickBooks until the valuation is certified. On Builder, homeowner invoices go across the same way.

• One invoice per valuation: the certified value, and the retention withheld as a minus line on the same VAT code, so the VAT falls on the net.
• The VAT code on each line comes from the project’s VAT treatment: 20%, 5%, zero, no VAT, or the domestic reverse charge.
• If your company has custom transaction numbers turned on, the invoice carries the next number in VariationFlow’s own series, and keeps it when the invoice is updated. If not, QuickBooks numbers it.
• The invoice carries the billing address held for the customer and falls due on the contract’s final date for payment.
• When QuickBooks shows the invoice fully paid, the valuation is marked paid with the date and method of the payment, usually within minutes. VariationFlow also looks every hour, and “Check for payment” looks straight away.

Before you connect

• VAT must be set up in QuickBooks (Taxes, VAT) before an invoice that charges VAT can go across. A company without VAT can still take invoices for projects set to no VAT.
• For a domestic reverse charge job, QuickBooks needs its “20.0% RC CIS” VAT code active. QuickBooks adds it as inactive when CIS is turned on; make it active under Taxes, Edit VAT, Edit rates, then the cog and Include inactive. VariationFlow says so if it is missing.
• Give each customer a billing address in VariationFlow, on the project or the customer record.

Connect it

1. Go to Settings, Integrations, choose “Connect QuickBooks Online”, sign in to QuickBooks and allow access to your company.
2. Under Post sales to, choose the product or service each invoice line posts to. Leave Post retention to as “Same as sales” unless you post retention separately.
3. Tick the box to send each valuation as soon as it is certified, or leave it clear and send each one yourself. Save.

Day to day

• Once a valuation is certified, “Send to QuickBooks Online” raises its invoice. Edit the valuation and the same invoice is updated, never a second one. If a send fails, the reason is shown beside it and the retry button sends it again.
• If the total in QuickBooks no longer matches VariationFlow’s figures, the valuation is not marked paid and the reason is shown beside it.
• Disconnecting clears the invoicing settings; set them again after you reconnect. If you disconnect from inside QuickBooks, the card in VariationFlow reads “Reconnect needed” the next time it is used.

Common mistakes

• Setting the wrong VAT treatment on the project. The QuickBooks invoice follows it.
• Sending a reverse charge valuation before the “20.0% RC CIS” code is active.
• Ignoring “Reconnect needed”. While the connection is down, invoicing stops until an admin reconnects.