How to Create Invoices and Match Customer Payments

Receipts tell you where your money went. Invoices tell you what still hasn't arrived.

Synceipt's invoicing lets you create invoices, track accounts receivable, and match customer payments directly to bank deposits. When a deposit lands in a connected bank account, Synceipt suggests which outstanding invoice it paid — including partial payments, and one deposit settling several invoices at once. That reconciliation is the part most invoice generators leave to you, and the reason this feature lives in a receipt-matching app rather than a separate product.

You can create invoices in Synceipt, or upload the ones you already produce in another tool. Either way they join the same accounts receivable workflow. This guide covers the whole loop, plus the accounting rule that decides when invoiced money counts as income and an honest list of what the feature doesn't do.

What You'll Learn

• Set up your invoice business details, letterhead, and numbering
• Create and issue a professional invoice
• Send an invoice from your own email account
• Upload invoices created in other software
• Match customer payments to bank deposits, automatically or by hand
• Handle partial payments and one deposit paying several invoices
• Track outstanding and overdue invoices with an aging breakdown
• Record cash payments, processing fees, and returned payments
• Understand how invoice payments affect cash-basis reporting

How Invoicing and Accounts Receivable Work in Synceipt

Synceipt already reconciles money going out. Invoicing is the same job pointed the other way, which is why the two workflows mirror each other exactly:

Invoices reach that workflow from two directions, and stop being distinguishable almost immediately:

Once an invoice is live, both kinds sit in the same list, get matched by the same engine, and roll into the same Outstanding, Overdue and Collected figures.

Step 1: Set Up Your Invoice Business Details

Do this once, before your first invoice. Your Synceipt account has your name and email, but no business identity — and that's what gets printed on the document your customer reads.

1. Open Invoices and choose Invoice settings.
2. Under Your business, enter your business name, billing email, phone, and address.
3. Upload a logo (PNG or JPEG) to print at the top of every invoice, if you use one.
4. Add your tax number and pick its type — VAT number, GST number, EIN — or leave it set to Not shown.
5. Under Numbering, set a prefix, the next number, and how many digits to pad to.
6. Under Defaults for new invoices, set your usual payment terms, currency, tax mode, and a standard customer note.
7. Choose Preview a sample invoice to see exactly what your customers will receive, then save.

Three details are worth knowing. Your tax number is stored encrypted and write-only — after saving, the field shows a masked hint rather than the number, and it's printed inside the PDF but deliberately kept out of the email body. Keep a copy of each invoice PDF is on by default, so you can always reopen exactly what a customer received. And the sample preview is built from what's on screen, unsaved edits included, so you can decide before you commit — it never consumes an invoice number.

How Invoice Numbering Works

The three numbering fields produce numbers like INV-1001. A number is never duplicated and never reused — a voided invoice keeps its number forever — and always increases. Numbers are assigned when you issue an invoice, not when you start drafting, so an abandoned draft never burns one.

Step 2: Create and Issue a Customer Invoice

1. Open Invoices and choose New invoice.
2. Select an existing customer, or type a new name and fill in what you have.
3. Set the issue date and payment terms; check the resolved due date shown underneath.
4. Add at least one line: description, quantity, optional unit, and unit price.
5. Add a discount, tax, customer note, private note, or project if you need them.
6. Choose Save draft.
7. Review it, then open its actions menu and choose Issue invoice.

What each of those steps is actually asking for:

1. 1

   The customer

   Their email address matters later — it pre-fills the recipient when you email the invoice. Synceipt warns you when a new name looks like a near-duplicate of one you already have, which is how you avoid ABC Corp and ABC Corp. splitting one customer's revenue between them.

2. 2

   Payment terms and the due date

   Terms run from Due on receipt through Net 7, 15, 30, 45, 60 and 90, plus Custom. Whichever you pick, the resolved due date appears under the field as a real date — Net 30 is the agreement, but a date is the answer. The due date is always editable, and typing one switches the terms to Custom. Terms are calendar days, and the date is fixed at issue, so changing your defaults later never moves an invoice you already sent.

3. 3

   The lines

   Each takes a description, quantity, an optional unit (hours, days, units) and a unit price. If you bill the same things repeatedly, save them once to Saved items — the equivalent of QuickBooks' Product/Service list — and pick them from the line's search box.

4. 4

   Discount and tax

   Discount is a flat amount off. Tax can be a percentage rate, an amount you enter yourself, or none — three modes, because a zero you typed deliberately means something different from no tax at all. You control the label, so it prints as VAT, GST or Sales Tax. A running Subtotal / Discount / Tax / Total sits at the bottom of the form.

5. 5

   Notes and project

   A note for the customer prints on the invoice; a private note doesn't. You can also attach the invoice to a Project, which ties the work back to the rest of your budgeting.

Saved, it's a draft: fully editable, no number yet, and counted nowhere. It doesn't appear in Outstanding, isn't matched against deposits, and affects no total. That's the point of it.

What Changes When You Issue an Invoice

Issuing is the one-way door. In a single step Synceipt draws the next number in your sequence, sets the due date, and locks the invoice's financial substance — amounts, line items, parties, number, and issue date. That lock is deliberate: your customer may now hold a copy, and editing the amount of INV-1005 afterwards creates two documents with the same number, which is the fastest way there is to lose an argument with an auditor. Corrections happen by voiding and re-issuing.

Voiding asks why, and keeps your reason on your record rather than the customer's copy. The number stays with the voided invoice permanently, and the original PDF isn't rewritten — a VOID watermark is applied at render time instead.

Step 3: Send an Invoice to Your Customer

Synceipt composes the message, attaches the PDF, and records that you sent it — but you send it from your own account. That's deliberate: a customer replying “can we split this across two POs?” needs to reach your business, not ours, and an invoice arriving from a third-party domain is weaker on trust before it's weaker on anything else.

1. 1

   Mobile

   Email invoice opens your device's mail composer with the recipient, subject, body and PDF already in place. Review it and send from your own Gmail, Outlook or iCloud account. With no mail account set up, it offers the share sheet instead of an error.

2. 2

   Web

   Where your browser can share files — Safari on macOS and iOS, Chrome on Android and Windows — you get a share sheet with the PDF genuinely attached. Everywhere else, Synceipt opens a pre-addressed email draft and downloads the PDF alongside it, because the mailto: standard has no field for an attachment. There's also a plain Download PDF button whenever you'd rather handle delivery yourself.

The message body changes with the invoice's state. An unpaid invoice reads as a bill. A partly paid one states the total and the balance, so a customer who already part-paid isn't invited to pay twice. A settled one says it's paid in full and thanks them; a voided one says it's cancelled and no payment is due. Your private notes, void reasons and tax number are never in it.

It also powers the most useful warning on the page: invoices you created and never sent carry a Not sent yet tag, and the summary counts them. An aging report structurally cannot show you that, and it's frequently the actual cause of the overdue column above it. Uploaded invoices are excluded, since they were emailed by whatever tool produced them.

How to Upload an Invoice You Made Somewhere Else

If you're happy with the invoices you already produce, you don't have to switch — upload them and use Synceipt for the receivables side.

1. On the Invoices page, choose Upload an invoice.
2. Pick the PDF or a photo of the invoice. Synceipt's AI reads the customer, number, dates, line items and totals into a draft.
3. Review the draft, answering anything it flags.
4. Choose Add to receivables to make it live.

It lands as a draft because the draft is the review screen. Before you accept it, Synceipt says what it couldn't read and asks about anything ambiguous: which existing customer this matches, whether two totals it found disagree, and whether the party it read as the customer is actually you — which is what happens when someone uploads a bill they received rather than one they sent.

• A number collision is flagged, not rejected: if another of your invoices already carries that number, you're told before accepting this one. External tools restart counters and occasionally do reuse a number, so it's a warning rather than a refusal
• That check catches the most common double entry: uploading the copy of INV-1042 your bookkeeper emailed back, when you generated INV-1042 here. A duplicate arriving under a different number isn't detected, so glance at your Outstanding total after a batch of uploads
• The original document is kept, and the card offers View original rather than View PDF so you always know which one you're looking at
• Uploads use one of your monthly document reads — the same pool your receipt scanning draws from — and the button tells you how many are left before you spend one. Creating an invoice in Synceipt uses no quota, because no AI is involved

Step 4: Match Customer Payments to Bank Deposits

This is the half that makes an invoice tracker worth having. When a deposit arrives in a connected bank account, Synceipt looks for the invoice it plausibly paid and puts a suggestion on the invoice itself: “$2,500.00 on 2026-08-20 may pay this,” with the bank description underneath and two buttons — Review, or Not this one.

1. Open Invoices. Any invoice with a suggested match shows it on the card.
2. Choose Review to open the payment dialog with the amount pre-filled, or Not this one to dismiss it.
3. No suggestion? Choose Apply a payment and search for the deposit by description or merchant.
4. Adjust the amount if this is a part payment, then confirm.

A suggestion never applies anything on its own. Review opens the ordinary payment dialog with an editable amount, and you confirm — that's the whole difference between a suggestion and a decision.

How Automatic Invoice Payment Matching Works

Three signals, weighted, with a confidence threshold a candidate has to clear before you're ever shown it:

• Amount — treated as a shape rather than a number. An exact match (within 50 cents or 0.5%) scores full marks; a smaller deposit scores half, because “it's smaller than the invoice” isn't evidence of anything; a larger one scores lowest
• Date — from 14 days before the invoice was issued to 90 days after it was due. The early window exists because retainers and deposits landing before the final invoice is written are normal in service work; the late one because a Net 30 invoice paid 60 days late is routine and still needs to match
• Reference — an invoice number in the bank description, or the customer's name against the merchant name. INV-00123, inv00123 and Invoice 00123 all read as the same reference

Two consequences make the difference between a matcher you trust and one you learn to ignore. A clean exact-amount match on a sensible date is suggested with no corroboration needed. But a deposit larger than the invoice is never suggested on score alone — a $5,000 batch ACH fits every invoice under $5,000, and that it could have paid your $600 invoice says almost nothing about whether it did. The one override is a distinctive invoice number in the bank memo, which is close to definitive.

Partial Payments and One Deposit Paying Several Invoices

Both are ordinary small-business bookkeeping, so both work from the start. The amount you apply is editable on every payment, so a customer who pays $3,000 against a $10,000 invoice leaves a $7,000 balance and the invoice reads as partly paid rather than paid or unpaid.

In the other direction, one deposit can settle several invoices — and Synceipt does the arithmetic. When a deposit exactly equals the sum of a small set of your outstanding invoices, it offers them as a set: “These three invoices add up to this deposit,” applied in one action. Exact sums only, and if two different subsets both add up it says nothing, because the arithmetic can't tell which is right and guessing while looking certain is the worst thing it could do.

Synceipt also refuses to let the same money count twice: it won't allocate more of a deposit than is left unapplied, and it won't let a deposit already linked to an inventory item sale be claimed as an invoice collection too.

Processing Fees and Sales Tax on a Net Deposit

A customer pays a $1,000 invoice through a card processor and $970 lands in your bank. Applied naively, that's a $30 mystery and an invoice that looks underpaid forever. Synceipt proposes the split instead — the invoice's taxable base as revenue, its tax as tax, and whatever the bank is short as a processing fee — reconciling to the deposit that actually arrived:

It stays quiet when there's nothing to say, and when the shortfall is too large to be a fee — that's a partial payment, and calling it a fee would invent an expense you never had.

How to Record a Cash or Check Payment

Record a cash payment handles money that never touches a connected bank account. It is not a “mark as paid” button: it creates a real cash transaction in your wallet and settles the invoice through the same path a bank deposit takes, so the income lands in your books and your cash balance. Enter the date the cash actually changed hands, not today — that decides which month the income falls in.

How to Handle Chargebacks, Bounced ACH Payments, and Returned Checks

All three are reversals rather than deletions. Open Payments & returns on the invoice and reverse the payment: the invoice goes back to outstanding, the payment is marked Payment returned, and both events survive in the record — a payment that arrived and then reversed really is two events, not a mistake to erase. Reversals can be partial, an accidental one can be undone, and where the return debit warrants it, Synceipt offers to record it against revenue.

How to Track Outstanding and Overdue Invoices

Four figures sit at the top of the Invoices page, each answering a different question:

Under those, a How late it is row breaks your receivables into standard accounts receivable aging buckets — Not due yet, 1–30, 31–60, 61–90, and Over 90 days. Each is clickable, filtering the list to the invoices behind it. A Revenue by customer card sits alongside, reading collected income rather than receivables — and it's where you'll notice a customer's revenue splitting across two near-identical spellings of their name.

• Filter by payment status (Outstanding, Overdue, Paid, All invoices), which is a different question from lifecycle state (Drafts, Issued, Voided) — both filters exist because both questions get asked
• Search by invoice number, customer, or project, and sort by issue date, due date, amount, or when it was added
• Export payments writes one CSV row per payment, dated by the deposit — the honest shape for a batch deposit that paid several invoices, and the one your accountant can reconcile

Under Cash-Basis Accounting, an Invoice Is Not Yet Income

Synceipt's reporting is cash basis. Issuing an invoice has no effect on your income totals — revenue is recognized when the customer's payment arrives — and the invoice is tracked as an expectation in its own receivables panel beside your profit and loss rather than inside it.

Worth stating plainly, because it's the opposite of accrual accounting, where issuing an invoice does recognize revenue and create a receivable. Synceipt doesn't offer accrual-basis reporting, so the cash-basis rule holds throughout — and it's what keeps the same money from being counted twice. One economic event, recognized once:

So Reports and your P&L reflect money you've actually collected, and the Invoices page reflects money you're still owed. If you close your books periodically, issuing, voiding, applying and reversing all respect a locked period — recording that you sent an invoice is the one exception, since a closed quarter is exactly when you're chasing its receivables.

Invoicing in More Than One Currency

Every invoice carries its own currency, defaulting to the one in your invoice settings rather than being hard-coded to dollars. Receivables are reported per currency and never summed across them, because an Outstanding figure folding euros into dollars would simply be wrong.

Matching requires the currencies to be equal: a USD invoice can't be paid by a EUR deposit, and Synceipt says so rather than inventing an exchange rate and quietly deciding what your customer paid. So invoice in the currency you'll be paid in.

What Synceipt Invoicing Does — and Doesn't Do

Synceipt is built for invoice tracking, accounts receivable, and payment reconciliation — not as a payment processor or a full accounting platform. The gaps below are deliberate rather than accidental:

If you need a customer portal, card payments on the invoice, or automated dunning, a dedicated invoicing platform is the right tool — and the upload path exists precisely so you can keep using one. What you get here is receivables that reconcile against your real bank activity, in the same place as the rest of your books.

Frequently Asked Questions