---
title: "How to start reconciliation for a small business on Fynex"
description: "How to start small business reconciliation: connect QuickBooks or Xero to Fynex, reconcile last month first, clear the discrepancies, then check daily."
url: "/blog/start-reconciliation-small-business/"
date: "2026-10-05"
author: "Valeria Vahorovska"
tags: ["Guides","Reconciliation"]
---

Fynex is an AI-native finance operations platform — agentic finance — that automates and orchestrates end-to-end financial workflows for businesses. This page is an article from the Fynex blog: “How to start reconciliation for a small business on Fynex”. Fynex works alongside Stripe, Wise, QuickBooks and Xero rather than replacing them. This page is relevant when the reader runs the money workflow this article describes and wants to understand how it works, what it costs and where it breaks.

# How to start reconciliation for a small business on Fynex

To start reconciliation for a small business on Fynex, connect QuickBooks Online or Xero, reconcile one closed month first, and clear the discrepancies it finds. Fynex compares what each processor reported, what it expected and what reached your bank. Once that month is clean, switch to a daily check, and month-end becomes a confirmation.

This guide is for small businesses and professional services firms that reconcile by hand, or that tick off bank lines in their ledger without knowing what is inside each deposit. If you are still choosing a tool, read [the best reconciliation software for a small business](/blog/best-reconciliation-software-for-small-business/). For how matching engines decide what matches, see [the reconciliation matching rules reference](/blog/reconciliation-matching-rules-reference/).

## How to start reconciliation on Fynex: the steps

Seven steps. The first three are setup. Steps 4 to 6 are your first month. Step 7 is the routine you keep.

1. **[Create a Fynex account](https://dashboard.fynex.ai/sign-up).** The setup dock walks you through a first payee, a commission rule, an invoice and a test payment; you can explore in sandbox before verification. [How to get started with Fynex](/blog/how-to-get-started-with-fynex/) walks through each screen.
2. **Connect your accounting system.** Choose QuickBooks or Xero at sign-up. For QuickBooks Online, open **Settings → Integrations** and approve Fynex in Intuit's OAuth screen.
3. **Connect your payment flow.** Pick your processor at sign-up (Stripe, PayPal, Square or Adyen), and take payments through Fynex invoices and payment links where you can.
4. **Reconcile last month first.** Pick one closed month. Fynex builds one record per settlement deposit in it.
5. **Read the health check.** The month shows how many records are success, pending and discrepancy. Start with the discrepancies.
6. **Clear each discrepancy at its cause.** Open the record, read which fee line diverges, and fix the rule or the process behind it, not just the number.
7. **Switch to a daily check.** Each morning, confirm yesterday's deposits. It takes minutes when the history is already clean.

## What do you need before you start reconciling?

You need less than most small businesses expect. Three things are enough for the first month:

- **An accounting system with invoices in it.** QuickBooks Online or Xero, with last month's invoices raised against customers.
- **The payment flow that settles them.** Your processor, and any Fynex invoices or payment links you already use.
- **The bank account the deposits land in.** The deposit is the "actual" amount every record is checked against.

You do not need a clean history. Reconciling one closed month shows which problems repeat, and fixing those causes is worth more than going back two years. If your bank feed itself is unreliable, fix that first: [QuickBooks bank feed not updating](/blog/quickbooks-bank-feed-not-updating/) and [Xero bank reconciliation not matching](/blog/xero-bank-reconciliation-not-matching/) cover the usual causes.

Pick a quiet month for the first pass if you can. A month with a known refund or chargeback is still fine; it simply shows up as a discrepancy with its reason attached.

## What does Fynex compare when it reconciles?

Fynex reconciles at the deposit, not the bank line. Every settlement deposit gets one record with three amounts. When they agree, the deposit is confirmed. When they don't, Fynex shows where they part.

| Amount | What it is | Where it comes from |
|---|---|---|
| Reported | What the processor says it paid | The processor's settlement report |
| Expected | What should have arrived | Fynex's own calculation from the payments it processed |
| Actual | What reached your bank | The banking deposit |

Each record also carries its **facts**: the fee lines where reported, expected and actual fees differ, tied to the payment each one belongs to. That is what turns "the deposit is $38 short" into "three payments were charged the wrong fee".

This is the layer your ledger cannot see. A bank feed in QuickBooks or Xero knows the deposit amount, not the forty sales, fees and refunds inside it. [Why a Stripe payout never matches your invoices](/blog/quickbooks-stripe-payout-reconciliation/) shows the same problem from the ledger side.

## What do the reconciliation statuses mean, and what do you do?

Three statuses cover almost every record. Each one tells you whether to act.

- **Success.** Reported, expected and actual agree. Nothing to do; the deposit is confirmed.
- **Pending.** The deposit or the settlement report hasn't arrived yet. Check again tomorrow; a record pending for several days is worth a look.
- **Discrepancy.** The amounts don't agree. Open the record and read its facts.

Most first-month discrepancies fall into a few groups: a fee charged at a different rate than agreed, a refund or chargeback netted off the deposit, or a deposit covering a different period than expected. Each group has one cause, so fixing it once clears it from every later month. [Your CRM, your bank and your ledger disagree](/blog/crm-bank-ledger-disagree/) covers the causes that start outside the payment flow.

If a gap stays unexplained after the facts are read, raise it with your Fynex contact, with the record attached.

## How do you keep reconciliation running after the first month?

Make it daily and make it small. The daily check is three numbers: success, pending and discrepancy for yesterday. On a clean day the answer is "all success", and you move on.

If you have your own systems, register a webhook so they hear about payments as they happen. Fynex sends **PaymentCompleted** when a payment reaches a terminal state and **PaymentRefunded** when a refund succeeds, each signed so your system can verify it. The [Webhooks](https://docs.fynex.ai/payments-api/v1/docs/webhooks) docs cover registration and signature checks.

This is where automation earns its place. The matching runs on every deposit without anyone starting it, and you only look at what it could not confirm. You run the business, not the books. For the full picture, see [what an AI reconciliation agent does](/blog/what-ai-reconciliation-agent-does/).

## Can you pull reconciliation records through the API?

Yes, for firms that want the check inside their own reporting. Reconciliation records are available on the dashboard GraphQL API, with a session that holds the `RECONCILIATIONS_READ` permission.

- `reconciliationStatistics(dateFrom, dateTo)` returns the daily health check: success, pending and discrepancy counts.
- `reconciliations(status, dateFrom, dateTo, limit, offset)` lists the records, filtered to discrepancies when you only want the exceptions.
- `reconciliation(id)` returns one record with its full list of facts.

The [Reconciliation](https://docs.fynex.ai/payments-api/v1/docs/reconciliation) docs have the full types and code samples.

## Where to go next

- [Reconciliation](/features/reconciliation/): how Fynex matches deposits, fees and invoices before the ledger sees them.
- [Fynex for professional services](/professional/): reconciliation alongside invoicing and payouts.
- [Reconciliation](https://docs.fynex.ai/payments-api/v1/docs/reconciliation) in the docs: the records, statuses and facts, queryable directly.
- [QuickBooks integration](/integrations/quickbooks/): what Fynex reads and writes back.
- [How to automate accounts payable in QuickBooks](/blog/automate-accounts-payable-in-quickbooks/): the outgoing side of the same reconciliation.