After I send an estimate to the client I take a 25% deposit before any work is carried out. How do I deduct the 25% from the estimate stage to when I send the invoice?

Hello and welcome to the Community, corkspraysw-outl

You can create an invoice for a percentage of the estimate by selecting Create invoice on the estimate > enter an amount in the % of each line field. (If you don't want to send an invoice for the deposit to the customer, simply select Save & Close after creating). 

When you're ready to issue an invoice for the remainder of the payment, open the estimate and click Create invoice, where you will see an option for Remaining total of all lines. 

For further support, check out our guide progress invoicing in QuickBooks Online. We'll be here if you need any additional assistance!