Invoicing Overview: Manual, Batch, and Automatic

Last updated October 16, 2026 · Admins and office staff

Billing > Invoices & Payments is your billing home base: every invoice and every payment for your company lives in one list there. There are three ways an invoice can come into existence (you type it in yourself, you run a batch, or the system creates it for you), and all three land in the same list where you review, send, and collect them. This article explains the three paths and when to use each, plus how payments and the Customer Portal fit in.

Before you start

  • An operator account with access to the Billing menu.
  • At least one customer (see Create a Customer). A manual invoice asks you to pick one of the customer’s jobs, or No job (one-off charge).
  • Priced work: per-visit and job-completion invoices bill the job’s product/service lines; monthly fixed and program round invoices bill the job’s accepted estimate. The more complete your customer → job → pricing chain, the more invoicing can do for you.
  • Optional: Payment Methods set up in Settings (Cash, Check, etc.) if you plan to record payments.

Your first invoice

A new company’s dashboard shows a Get to your first paid invoice checklist: add your company address and phone, set your sales tax rate (or turn sales tax off), add a service with a price, add your first customer, add work for that customer, create and send the invoice, and record the payment. Done steps are ticked and the next one has a button. The checklist goes away once you record your first payment, or 30 days after you sign up, whichever comes first.

The three ways invoices get created

1. Manual invoices (one at a time)

Click Create invoice on Invoices & Payments (or Create Invoice on a job’s Financials tab), pick the customer and the job (or No job for a one-off charge), add line items, and save. Best for one-off work, custom amounts, or anything that doesn’t follow a standard billing pattern. When the invoice is for a job, a tick box asks whether this is the final bill for the job; tick it to move the job to Invoiced, leave it for a deposit or progress bill. See Create and Manage Invoices.

On a Per Visit job you can also choose a completed visit under Visit. The invoice then counts as that visit’s bill, so batch and automatic invoicing will not bill that visit again. With no visit chosen, a manual invoice is an extra charge on top of the job’s normal billing.

2. Batch billing (you press the button)

The Batch billing section on Invoices & Payments and the buttons on a Program’s summary page generate many invoices at once from work that’s already done:

  • Generate Visit Invoices — one invoice per completed, not-yet-invoiced visit on Per Visit jobs.
  • Generate Monthly Fixed — one invoice per Monthly Fixed job for the current month.
  • Program round invoicing — one invoice per customer for a completed program round (fertilization/PHC programs).

You choose when to run it; the system figures out what’s billable and skips anything already invoiced. See Batch Billing.

3. Automatic invoicing (the system presses the button)

Turn on Set Job Invoicing on a job, and the system creates invoices for that job on its own: when a visit is marked completed (Per Visit), at the start of each month (Monthly Fixed), or once when the job is completed (On Job Completion). Invoices are created for your review only. Nothing is ever emailed or charged to the customer automatically. See Automatic Invoicing.

How payments fit in

Money is recorded against invoices as payments. A single payment can cover one invoice or be split across several of a customer’s open invoices. You can record payments three ways:

  • Record payment on a list row: the quick way, right from the Invoices & Payments list, on any invoice row with a balance.
  • Record Payment screen: the full payment screen, for splitting one check across multiple invoices.
  • Online via the Customer Portal — the customer pays you directly (see below).

When an invoice is fully paid it’s flagged Paid. If it’s linked to a job whose work is done (Completed or Invoiced) and no other invoice on the job still owes money, the job is moved to Closed. A deposit a customer paid on an estimate sits on their account as credit on account until you apply it to an invoice. See Record Payments.

How the Customer Portal fits in

If you’ve enabled the Customer Portal and connected Stripe, customers can view and pay their invoices online, with an optional card-processing surcharge passed through to the customer if you’ve turned that on. You don’t have to do anything when this happens:

  • The payment appears in your list automatically with an Online badge (manually keyed payments show Manual).
  • If there’s been any online activity, the top of the page shows an Online Payments / Manual Payments breakdown, plus Customer-Paid Processing Fees collected.
  • A refund or a dispute you handle in Stripe is recorded here on its own: a refund shows as a Refund row, and money a dispute takes back comes off the invoice, which owes it again.

Setup and details are covered in the portal guides — see the Customer Portal overview, Merchant setup, and Stripe Connect.

Reading the Invoices & Payments list

Chips across the top pick what you see: Open, Recent, Overdue, Not sent, Paid, All history, and Unbilled work (which opens the Unbilled work page). You can also enter an exact Date range. Unpaid invoices are always included, however old.

Every row is either an Invoice or a Payment (the Type badge tells you which; a refund reads Refund). The Sent column shows how and when an invoice went out, or Not sent. Invoice rows carry a live status:

Status Meaning
Open Unpaid, not yet past the due date.
Overdue Unpaid and past the due date.
Partial Some money received, balance still owed.
Paid Paid in full.
Overpaid Payments recorded exceed the invoice total.

All amounts show dollars and cents. The grid supports search, filtering, sorting, grouping, and export to Excel, PDF, or CSV from its toolbar, which is handy for handing data to your accountant.

What happens next

A typical invoice’s life: it’s created (manually, by batch, or automatically) → you review it on its summary page → you Send invoice, print it, or Mark as sent → the customer pays (online or otherwise) → you record the payment (or the portal records it for you) → the invoice flips to Paid and, if the job’s work is done, its job closes. Start with Create and Manage Invoices to walk that path end to end.

Tips & best practices

  • Price jobs before relying on batch or automatic invoicing. Per-visit and job-completion billing need the job’s product/service lines; monthly fixed and round billing need an accepted estimate.
  • Set Invoicing Terms (days) on each job. Generated invoices compute their due date from the job’s terms (falling back to 30 days). Manual invoices default the due date to 30 days out, adjusted to the job’s terms once you pick a job.
  • Pick one primary path per job. A job set to Per Visit with auto-invoicing on doesn’t also need you running visit batches for it — batch billing remains useful for jobs you haven’t opted in.
  • Work the Not sent chip. Generated invoices are drafts until you send them.
  • Use the Type filter on the grid to look at just invoices or just payments when reconciling.

Troubleshooting

  • “Where do I set tax rates or invoice defaults?”: Company-wide invoice preferences (Qty/Rate columns, Product/Service column, sales tax on/off and rate) come from your company settings and can be overridden per invoice under Invoice Settings on the create form.
  • An invoice I expected wasn’t generated: check the job’s Billing Mode, that the visit/round is actually marked completed, that the job has the pricing that mode uses, and that the visit isn’t already invoiced or marked as billed. The Unbilled Visits report gives the reason per visit. Details in Batch Billing and Automatic Invoicing.
  • A payment shows “Online” but I never entered it — that’s a portal payment via Stripe; it’s real money and needs no action from you.
  • “Sent history could not be loaded, so nothing is marked Not sent.”: a temporary problem reading send history. Nothing is lost; reload later.

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