How do I set the payment method for invoice I send out via the Quickbooks app? My website-written invoices successfully let people pay via PayPal, but not with the app.

Welcome to the Community forum, @alex90.

When sending invoices via QuickBooks Online app, make sure you're using the same invoice template when sending it via website. Since as long as the template is the same, what you can do in the website is the same on the app. 

Moreover, I invite you checking our Manage Customers and Income page. It contains great articles and learn some best practices in managing your payments effectively.

If you have any other questions about this, get back to me by commenting below. I'd be more than happy to answer it for you. Have a wonderful day ahead!

Thank you for your reply.

Am I supposed to be able to choose the payment methods for an invoice in the app? There seems to be no way to specify what the payment method should be.

I do believe I’m using the same invoice template in the app as on the website, but getting different results.

Thanks for posting in the Community, alex90.

You can only select a payment method once you receive payment for an invoice. Let me walk you through the steps:

1. Click the Sales tab on the left menu.
2. Go to the Invoices tab.
3. Select the invoice.
4. Under Actions, click Receive payment to pay an invoice.
5. Click the drop-down arrow under the Payment method field.
   
6. Check the invoice number that you want to pay.
7. Click Save and close.

For future reference, you can reconcile your account to match your credit card and bank statements. Please visit this article: Reconcile An Account In QuickBooks Online.

You can touch base if you need further assistance.