Your First Invoice in Biller Genie

New to Biller Genie? Walk through what to set up before your first invoice goes out, the QuickBooks workflow shifts, and what your customer experiences.

Written by Thomas Aronica (Super Administrator)

Updated May 24th, 2026

Biller Genie is designed to work with the accounting software you already use. You keep creating invoices in QuickBooks Online, QuickBooks Desktop, or Xero the same way you always have. Biller Genie syncs each invoice over and takes care of getting it to your customer, collecting payment, applying reminders if needed, and posting the payment back to your accounting software. This guide walks through what to set up before your first invoice goes out, and how the day-one workflow changes (in small ways) once Biller Genie is on.

Set up these defaults FIRST

Before any invoice syncs over, configure two things. They're quick (under 15 minutes each) and they shape every invoice Biller Genie sends.

Setting Global Customer Defaults — decides what payment methods customers can use, whether autopay is required, late-fee policy, and which reminders go out and when. This is the behavior layer.
Setting Invoice Defaults — decides what your invoice looks like: which columns show, the template (Classic / Modern / Simple), the footer message, whether the PDF includes a payment QR code. This is the appearance layer.

Optional but useful

If you have meaningfully different customer groups (premium vs. standard, retail vs. wholesale, etc.) set up Customer Type Defaults too. Otherwise you can come back to that later.

What changes in your day-to-day workflow

Biller Genie owns the invoice-to-cash cycle — sending the invoice, taking the payment, reminding the customer, posting back. So your accounting software stops doing those things. The day-to-day shifts are small but they matter:

QuickBooks Online merchants

When you finish an invoice in QBO, click Save and close instead of Save and send. Save and send tells QBO to email the invoice itself, which creates a duplicate (your customer would get the QBO email AND the Biller Genie email). Save and close just saves the invoice; Biller Genie picks it up on the next sync and handles the send.
Turn off automatic invoice emailing in QBO. In QBO, go to Account and Settings > Sales and disable any "automatically send" toggles. Biller Genie is the sender now.
Don't manually email invoices from QBO. If you do, the customer will get the QBO version PLUS the Biller Genie version when Biller Genie syncs the invoice and sends. Stick to Biller Genie's send flow once you're on.

QuickBooks Desktop merchants (MagicCarpet)

Create invoices the same way you always have. MagicCarpet picks up new invoices from your company file on the next sync and pushes them into Biller Genie.
Don't email invoices directly from QuickBooks Desktop. Same reason as QBO — Biller Genie is the sender. QBD's "Send" or "Email" actions duplicate the message your customer receives.

Why "two invoices" happens

If your customer gets two emails, it's almost always because either (a) QBO auto-sends are still on, or (b) the invoice was clicked "Save and Send" instead of "Save and Close" in QBO, or (c) the merchant emailed manually from QuickBooks Desktop. Turn off the accounting-software send paths and let Biller Genie own the send.

What happens when Biller Genie sends the first invoice

Sync picks up the invoice. Within minutes (QBO) or on the next scheduled sync (QBD), the invoice lands in Biller Genie.
Biller Genie renders the invoice using your Invoice Defaults. The columns, template, footer message, and QR code (if enabled) all come from the defaults you set up earlier.
The customer gets an email. The email contains a "View Invoice" link that opens the invoice in your branded Customer Portal. From there they can pay by card, ACH, or whatever methods you've allowed in Customer Defaults.
Reminders fire automatically. If the customer doesn't pay, Biller Genie sends reminders on the schedule you configured. You don't have to chase the invoice manually.
Payment posts back. When the customer pays, Biller Genie processes the transaction through your gateway and posts the payment back to QuickBooks. The invoice closes in both systems.

Customize defaults for specific customers

Once your global defaults are dialed in, you'll find specific customers that need different treatment — VIPs who shouldn't get late fees, big customers who need autopay required, a one-off who wants paper invoices. Use Per-Customer Overrides to handle those without changing your global defaults. For larger groups of customers that all need the same different setup, use Customer Type Defaults to set them up by QuickBooks customer type.

What your customer experiences

The first email your customer gets from Biller Genie is from your business, branded with your logo and colors. They click View Invoice, land in the Customer Portal, and pay. Most customers complete the whole flow in under two minutes. See Using the Customer Portal for the full customer-facing walkthrough.

Frequently asked questions

Do I still create invoices in my accounting software, or in Biller Genie?

Keep creating in your accounting software. Biller Genie is a layer on top — it doesn't replace QuickBooks. The only practical change is to stop sending the invoice from QuickBooks (Save and Close instead of Save and Send in QBO).

What if I want to create an invoice directly in Biller Genie?

You can. Open the Invoice Generator in Biller Genie and create the invoice there. It syncs back to your accounting software on the next sync. See How To Create An Invoice.

Can I manually send a specific invoice from Biller Genie?

Yes. Open the invoice in Biller Genie and click Send Invoice from the top menu. The automatic reminder cadence still applies after that. See How to Send an Invoice Manually.

My customer never got the first invoice. What now?

Check three things: (1) the customer's email on file is correct in your accounting software, (2) the invoice synced into Biller Genie (look in the Invoices list), (3) the email didn't bounce or land in spam. Biller Genie has a Bounced Email Report that flags delivery failures.

How long does the initial sync take?

QuickBooks Online: usually under 30 minutes for an average-sized customer base. QuickBooks Desktop via MagicCarpet: depends on your sync interval (configurable, usually every 5 to 15 minutes) and the size of your company file. Talk to your implementation contact if you need to estimate.

Setting Global Customer Defaults — the behavior settings to lock in first.
Setting Invoice Defaults — the appearance settings to lock in first.
Customer Type Defaults — when you need different settings for different groups.
Per-Customer Overrides — different settings for a single customer.
Connecting QuickBooks Online — the initial setup walkthrough for QBO.
Connecting MagicCarpet to QuickBooks Desktop — the initial setup walkthrough for QBD.
How To Create An Invoice — creating a one-off invoice directly in Biller Genie.
How to Send an Invoice Manually — manually sending or resending an invoice.
Using Reminders — the reminder cadence Biller Genie applies after the send.