Automated Shopify Reconciliation & Settlement Matching
Reconcile gross order values against net bank deposits across Shopify Payments, PayPal, and buy-now-pay-later schemes with automated Shopify fee deductions.
Automate payout reconciliation for Shopify stores
Automate your end-to-end Shopify reconciliation across Shopify Payments, PayPal, and Klarna down to the penny. Automatically separate Shopify fees, sales taxes, and refunds before posting to your ledger.
Multi-channel clarity for high-volume Shopify brands
Stop losing hours to manual bank matching. Equali provides automated Shopify reconciliation, syncing orders, processing fees, and bank payouts continuously so your accounting ledger always reflects reality.
Direct Shopify Ledger Journal Entries
Post categorised journal entries directly into Xero, FreeAgent, QuickBooks, or NetSuite with Shopify fee, VAT, and shipping breakdowns.
AUDIT ENTRY#10432
Posted · Verified
Gross Sale£49.99
VAT (20%, incl.)£8.33
Processing fee (2.9%)−£1.45
Net Payout SettledMatched to bank MT940
£48.54Audit Ref: AUD-2026-9921Posted to Shopify · 14 Jun
Zero-touch fee & tax allocation
Processing fees, domestic VAT, and cross-border taxes are split automatically on every transaction.
Penny-perfect discrepancy alerts
Surface unallocated payouts, unexpected processing deductions, and missing bank deposits immediately.
Historical transaction backfill
Ingest and reconcile up to 12 months of Shopify sales and payout history in a single sync.
Multi-currency settlement support
Handle foreign exchange differences and payouts across multiple currencies with automated gain/loss calculations.
AUDIT TRAIL#TX-94021
100% 3-Way Matched
01
Shopify Order#10432
12 Jun · Online Checkout£49.99Gross Sale
02
Stripe Gatewaych_3N84x
Fee deducted: −£1.45 (2.9%)£48.54Net Captured
03
Barclays SettlementMT940
Payout po_941 · 14 Jun£48.54Settled In Bank
Variance: £0.00 (Zero Break)Ledger: Xero JE-8892
Audit-grade visibility from order to bank deposit
Engineered for eCommerce operators who demand exact reconciliations without the spreadsheet burden. Every matched transaction preserves an immutable link between the Shopify order ID, the gateway payout transfer, and the accounting journal entry. Easily handle returns, partial refunds, chargebacks, and adjustments without breaking your month-end close.
Connect Shopify in three simple steps
Connect your store and accounting platform in minutes. Zero custom code or developer resources required.
- 01
1. Connect Shopify Store
Authorise the Equali Shopify connector with one click to begin automated transaction and payout ingestion.
Integrations & FeedsXXeroAccountingConnectedShopifySales FeedActiveStripePSP FeedActive - 02
2. Map Chart of Accounts
Select your sales clearing accounts, gateway fee expense lines, and tax liability codes in our visual rule mapper.
Automated 3-Way Match#REC-2025-03Shopify Order #104214:22 · Gross Sale£1,240.00✓ Order verifiedStripe ch_3N82...14:23 · Net + £28.48 fee£1,240.00✓ Gateway settledBank Feed Payout #PO-99116:05 · Statement Feed£1,240.00Matching...✓ Matched - 03
3. Reconcile Continuously
Transactions are ingested continuously, settlements are matched automatically, and balanced journals post directly to your ledger.
Exception Triage31 Mar1✓-£185.00Chargeback discrepancyDisputed transaction hold · Order #1089
Assignee:Assign to...▾SJSarah JenkinsAssign ColleagueSJSarah JenkinsSenior FinOpsDMDavid MillerFinancial Controller
MonthlyAnnual Save ~17%
Lite
$23/mo$19/mo
Not available at this volume
1 month of history on setup
- 1 sales or payment integration
- 2 click journal entry posting
- Settlement reconciliations
- Dashboard & standard reports
- Payment Search
- Tax Items
Pro
$47/mo$39/mo
Not available at this volume
6 months of history on setup
- Everything in Lite
- Up to 3 sales or payment integrations
- Slack support
- Daily, weekly or monthly scheduled reports
- Multi-Store Support
Premium
$119/mo$99/mo
Not available at this volume
12 months of history on setup
- Everything in Pro
- Unlimited sales or payment integrations
- Custom reporting
- Ad-hoc Reports
- File Upload
$Custom
Scalable enterprise solutions for more complex requirements
- Everything in Premium
- Unlimited stores
- Unlimited payment providers
- Unlimited sales channels
- Unlimited integrations
- Custom API access integrations
- Priority phone & Slack support
- Custom onboarding & training
Compare all features
| Feature | LiteStart trial | ProStart trial | PremiumStart trial | EnterpriseBook a demo |
|---|---|---|---|---|
| Sales & Payment IntegrationsIncludes eCommerce platforms (e.g. Shopify) and payment providers (e.g. Stripe, PayPal). May require additional setup. | 1 | 3 | Unlimited | Unlimited |
| Accounting IntegrationsIncludes accounting systems (e.g. Xero). May require additional setup. | ||||
| ERP IntegrationsIncludes ERP platforms (e.g. NetSuite). May require additional setup. | Enterprise Only | Enterprise Only | Enterprise Only | |
| Data Update FrequencyHow frequently payment and order data is refreshed via API (where available). | Every 15 minutes | Every 15 minutes | Every 15 minutes | Every 15 minutes |
| Historical Data (On Setup)Amount of past payment/order data processed during initial setup (via API where possible). | 1 month | 6 months | 12 months | 12 months |
| Upload FilesUpload and map CSV, XLS, XLSX or TXT files directly in the Equali dashboard. | - | - | ||
| Multi-Currency SupportReconcile and report on transactions in multiple currencies. | ||||
| Multi-Entity SupportManage and reconcile data across multiple legal entities, subsidiaries or stores in one account. | - | |||
| Custom IntegrationsBespoke API connectors or custom development for proprietary or unique systems. | Enterprise Only | Enterprise Only | Enterprise Only | |
| Custom WorkflowsBespoke workflow setup for your specific use case. | Enterprise Only | Enterprise Only | Enterprise Only | |
| Categorisation & Tagging For Journal EntriesRevenue sub-ledger with categorised breakdowns for posting to specific journals (revenue, fees, etc). | ||||
| Journal Entry PostingDirectly post categorised journal entries to your linked accounting system. | ||||
| Link Journal Entries To Orders/PaymentsTrace and link posted journal entries back to the original order or payment record. | ||||
| Settlement ReconciliationReconciles settlements vs individual payments and related entries. | ||||
| Payment ReconciliationMatches payments from providers with orders from eCommerce platforms, including refunds and chargebacks. | - | - | ||
| Payment SearchSearch for any payment or order using several data points directly from the dashboard. | ||||
| Advanced Reconciliation ToolsBrowse reconciliation results, review reports, resolve breaks and understand why they occurred. | - | - | ||
| Custom Reconciliation RulesCustomisable reconciliation rules, including rule suppression, tolerance thresholds and more. | Enterprise Only | Enterprise Only | Enterprise Only | |
| Cross-Platform ReconciliationsReconciliations across platforms e.g. Shopify orders reconciled with PayPal payments. | Enterprise Only | Enterprise Only | Enterprise Only | |
| Reconciliation Approval WorkflowA second approver reviews and authorises reconciliation changes before they take effect. | - | - | - | |
| CASS ReconciliationsSpecialised reconciliation workflows for CASS 15 safeguarding reconciliation and reporting. | Enterprise Only | Enterprise Only | Enterprise Only | |
| Split Settlements At Month-EndSplit a settlement that spans a month end so each period's figures are accurate. | - | |||
| Customisable Analytics DashboardCustomisable analytics dashboard with advanced filtering, KPIs and reconciliation breakdown. | ||||
| ReportingStandard and customisable scheduled and on demand reporting. | Standard | Standard | Custom | Custom |
| Scheduled ReportsAutomated reports delivered on a chosen cadence (daily, weekly or monthly) via the dashboard. | Monthly | Daily, Weekly or Monthly | Daily, Weekly or Monthly | Daily, Weekly or Monthly |
| Ad-hoc ReportsGenerate custom reports on demand without waiting for a scheduled run. | - | - | ||
| Flexible Custom FieldsAdd customisable metadata fields to reporting data for better filtering and reporting. | Enterprise Only | Enterprise Only | Enterprise Only | |
| Manual Financial EntriesAdd one-off financial entries directly, outside the automated feed, for cases the connectors don't cover. | - | - | ||
| Tax ItemsMapping and categorisation of tax rates and items from sales channels and payments, for accurate tax reporting and journals. | ||||
| Transaction ViewBreakdown of each transaction, showing all financial entries associated with the order, including sales, refunds, fees and tax. | ||||
| CASS DashboardDedicated view and analytics for CASS reconciliation. | Enterprise Only | Enterprise Only | Enterprise Only | |
| Help and supportAvailable support channels and documentation. | Help centre & support chat | Help centre, support chat & Slack | Help centre, support chat, Slack & phone | Help centre, support chat, Slack & priority phone |
| Accountant AccessDedicated read-only or restricted logins for accountants and external advisors. | ||||
Ready to get started?14-day free trial on self-serve plans | PremiumStart 14-day trial | EnterpriseBook a demo | ||
Trusted by high-growth eCommerce merchants
"Reconciling Shopify payouts across multiple payment gateways used to take us days every month. With Equali, every payout matches the bank deposit automatically down to the penny."
Head of FinanceGlobal DTC Brand
Related reading & guides
Explore technical guides and architectures for automated reconciliation and accounting.
Accounting6 min read
What is journal entry automation?
Journal entry automation creates the categorised accounting entries for your sales, fees, refunds and payouts without anyone typing them, and reconciles them back to the orders and settlements they came from.
Martin Burn · 22 July 2026Strategy6 min read
Build vs buy: automated reconciliations
Should you build automated reconciliations in-house or buy an off-the-shelf specialist product? The factors to weigh, from opportunity cost and complexity to maintenance.
Martin Burn · 23 July 2026Frequently asked questions about Shopify reconciliation
What is Shopify reconciliation?
Shopify reconciliation is the automated process of matching gross Shopify store orders, processor fees, refunds, and adjustments directly against net bank payout deposits and general ledger accounts, eliminating manual spreadsheet matching.
How does Equali reconcile Shopify payouts to bank statements?
Equali extracts transaction-level data directly from Shopify and payment providers (Shopify Payments, PayPal, Klarna). It matches the gross order amounts, subtracts processing fees and refunds, and reconciles the resulting net payout amount against your bank statement feed automatically.
Does Equali support multiple payment gateways on one Shopify store?
Yes. Many stores use Shopify Payments alongside PayPal, Klarna, or manual payment methods. Equali reconciles each gateway's independent payout cycle and settlement schedule into the correct clearing accounts.
How are refunds, chargebacks, and adjustments handled?
Refunds and dispute fees are matched against the specific payout batch in which the gateway deducted them. Equali posts reversing entries to the appropriate revenue and fee accounts, preserving an exact audit trail for every transaction.
Which accounting platforms does Equali support for Shopify?
Equali provides direct API integrations for Xero, FreeAgent, QuickBooks Online, and Oracle NetSuite, as well as exportable flat files and custom ERP feeds.
Stop chasing reconciliations in spreadsheets
Connect your channels and providers, and let Equali reconcile, categorise and post every transaction. Start free, or see it on your own data.