Transaction Reconciliation for Per Transaction Sync: How to verify data from your platforms in Synder

• What this guide is for
• How to confirm it worked
• Supported integrations and automation levels
• How to reconcile Stripe, Shopify, and Amazon (Automated)
• How to reconcile PayPal transactions (Assisted)
• How to reconcile other integrations (Manual)
• Understanding your results
• How Synder matches transactions
• Managing your reconciliations
• Limitations & Important Notes
• FAQ

What this guide is for

Important: this guide is for Per Transaction Sync users. If you use Summary Sync, use the separate Summary Sync Transaction Reconciliation guide instead, because the comparison logic, timing, and fixing process are different: Transaction Reconciliation for Summary Sync.

Synder’s Transaction Reconciliation tool compares the data in your accounting software against the original records from your payment platform. As a result, it shows you exactly which transactions matched, which have amount differences, and which are missing. As a result, you can close out periods with confidence.

Use this if:

• You use Per Transaction Sync
• You need to finalize month-end close and want certainty that no transactions are missing or mismatched

Don’t use this if:

• You use Summary Sync — use the separate Summary Sync Transaction Reconciliation guide instead
• You need help with bank reconciliation inside GL (QuickBooks, Xero, Oracle NetSuite)

Prerequisites:

• At least one integration (Stripe, PayPal, Shopify, Amazon, etc.) connected to Synder
• An accounting platform (QuickBooks Online, Xero, Oracle NetSuite) connected to Synder
• Transactions already synced for the period you want to reconcile

How to confirm it worked

Your reconciliation is complete when nothing is left unresolved in the Discrepancy and Missing source tabs.

A transaction counts as resolved either when you fix it or when you move it to Ignored — ignored transactions no longer hold the reconciliation open. Once nothing remains, the status changes to “Reconciled”.

If items remain, you can resolve them, or ignore the ones that are non-material.

How does Synder reconcile?

Synder compares your chosen account report from GL against the payment platform report. This directly verifies that what is recorded in your books matches the original payment platform data.

Supported integrations and automation levels

The level of automation depends on your payment platform. Specifically, there are three modes:

Automated — Synder downloads files from both the payment platform and your accounting software automatically. No file uploads needed.

Assisted — You upload a specific predefined report from the payment platform. Synder handles normalization, column mapping, and comparison automatically.

Manual — You upload any CSV or XLSX file (up to 100 MB) and manually map the columns to the required fields.

Mode availability by platform

Platform	Automated	Assisted	Manual
Stripe	✅	✅	✅
PayPal	❌	✅	✅
Shopify	✅	✅	✅
Amazon	✅	✅	✅
All other integrations	❌	❌	✅

For Automated and Assisted modes, Synder assigns column mappings automatically. You do not need to map anything manually.

How to reconcile Stripe, Shopify, and Amazon (Automated)

For Stripe, Shopify, and Amazon, reconciliation is fully automated. Synder downloads both the payment platform data and your accounting file without any manual steps.

• Go to Transactions → Transaction Reconciliation in the left sidebar.
• If this is your first reconciliation, click “Run audit” on the welcome page. Otherwise, click “Run reconciliation” in the top-right corner.

• Set the date range for the period you want to reconcile. Note: you cannot select today’s date — the payment platform may not have finalized today’s transactions yet.

• Under Accounting, Synder pre-selects your connected accounting platform. Set the Automation mode to “Automated”.
• Under Integration, select your payment platform (Stripe, Shopify, or Amazon).
• Select the Account to reconcile for your transactions.
• Set the Integration Automation mode to “Automated”.

Note: You’ll also see an “Any account” option in the Integration dropdown. This covers accounts that are not associated with a specific integration. To learn how to reconcile these, see the Manual reconciliation section below.

• Click “Start matching”.
• Synder automatically downloads the relevant reports from your payment platform and your clearing account details from your accounting software. This process may take a few minutes to an hour, depending on transaction volume.
• Once processing is complete, you will see your results. See “Understanding your results” below.

Platform notes:

• Shopify — reconciliation covers the Shopify Payments clearing account only. This does not include other payment gateways like manual orders or POS with external payment methods.
• Amazon — in multicurrency setups, a small number of payouts synced in pre-converted currency may appear as unmatched. This is expected behavior, not an error.

How to reconcile PayPal transactions (Assisted)

PayPal does not support automatic report downloads. You need to upload your PayPal report manually. After that, Synder handles everything else.

• Go to Transactions → Transaction Reconciliation in the left sidebar.
• Click “Run reconciliation” (or “Run audit” if this is your first time).
• Set the date range for the period you want to reconcile.
• Under Accounting, set the Automation mode to “Automated” (Synder will pull this file automatically).
• Under Integration, select PayPal.
• Select the Account to reconcile for PayPal transactions.
• Set the Integration Automation mode to “Assisted”.
• You will see instructions for which report to download. Follow these steps:
  • Log in to your PayPal account.
  • Go to Reports → Activity Download.
  • Select “Balance affecting” as the transaction type.
  • Set the date range to match your reconciliation period.
  • Download the report in CSV format.
• Then, upload the downloaded file to Synder using the file upload area.

Note: The Account to reconcile list is grouped by the reconciliation mode each account supports. PayPal accounts that Synder created appear under Synder accounts (assisted reconciliation); every other account appears under Synder accounts (manual reconciliation) and can only be reconciled manually. Pick the account first — the group it sits in tells you which modes are available.

• Click “Start matching”.
• Synder then normalizes both files, maps the columns, and runs the comparison automatically.
• Once processing is complete, go ahead and review your results.

How to reconcile other integrations (Manual)

To reconcile an account that is not tied to a specific integration, select “Any account” from the Integration dropdown — it sits at the bottom of the list. This option shows all accounts in your books under Manual mode, with no integration bound. Additionally, Manual mode works for any integration that doesn’t support Automated or Assisted modes. If you have a transaction report in CSV or XLSX format from any payment platform, you can upload it and Synder will run the comparison. This includes platforms like Square, WooCommerce, and HubSpot, as well as any other account you want to reconcile as long as you can export a transaction file from it.

• Go to Transactions → Transaction Reconciliation.
• Click “Run reconciliation”.
• Set the date range.
• Under Accounting, set the Automation mode to “Automated” (or “Manual” if you want to upload your own accounting file too).
• Under Integration, select your payment platform.
• Set the Integration Automation mode to “Manual”.
• Upload your CSV or XLSX file (up to 100 MB).

• Click “Map columns”. You will see a list of fields — some are mandatory (Primary ID, Amount, Date) and others are optional (Secondary ID, Transaction type, Description, Currency).
• Map each required field to the corresponding column in your file.
• Optional: Save your mapping as a template so you can reuse it for the same integration in the future.
• Click “Apply mapping”, then “Start matching”.

• Review your results.

Understanding your results

After the comparison is complete, Synder organizes your results into four tabs:

Matched

These transactions appear in both sources with matching IDs and amounts. They are fully reconciled. No action needed.

Each row is one match, not one transaction. Matching ID is the identifier Synder matched on, Total amount is the net amount of the match, Types lists the transaction types involved on both sides, Match type shows how the match was made — Auto, Assisted or Manual — and Count is how many rows make up the match, counting both sides together.

Expand any row to see the underlying entries split into Accounting rows and Integration rows, each with its Date, Primary ID, Secondary ID, Transaction type and Amount.

The two sides often hold different numbers of rows, and that is normal — your accounting records frequently break a single platform transaction into separate entries. For example, one Stripe charge of 766.79 USD appears on the integration side as a single row, but on the accounting side as two: a Payment of 790.00 USD and an Expense of -23.21 USD for the processing fee. Together they net to the same 766.79, so Count reads 3.

Discrepancy

These transactions matched by ID, but the amounts differ. Therefore, review them to understand the cause. For instance, common reasons include partial payments, currency differences, or fee adjustments.

Missing source

These transactions could not be found in the opposite source. The tab splits into two sections:

• Missing in accounting — transactions that exist in the payment platform but not in your accounting records. They may have been skipped during sync, excluded by a filter, or fall outside your sync date range.
• Missing in integration — transactions in your accounting records that were not found in the payment platform report.

Additionally, each section has its own search, date range, amount and currency filters to help you investigate.

Can’t resolve an unmatched transaction automatically? If you know a transaction in one source corresponds to an entry in the other, you can pair them manually and keep a full audit trail. See How to Use Manual Matching in Transaction Reconciliation.

Ignored

These are transactions you manually marked as ignored. Use this tab for known or non-material discrepancies.

To move transactions here, tick them in the Discrepancy or Missing source tab. A bar appears showing how many you’ve selected and their combined total — click Ignore to move them all at once, or Clear all to start over. Missing in accounting and Missing in integration each keep their own separate selection.

You can un-ignore transactions at any time and they return to their original category.

How Synder matches transactions

Synder runs a three-pass comparison based on transaction IDs:

1. Pass 1: Primary ID (Accounting) ↔ Primary ID (Platform)
2. Pass 2: Primary ID (Accounting) ↔ Secondary ID (Platform)
3. Pass 3: Secondary ID (Accounting) ↔ Secondary ID (Platform)

When Synder finds a match, it groups all related rows by that ID. Then it compares the total amounts. If the totals match, the group goes to Matched. If the totals differ, it goes to Discrepancy. If no match is found after all three passes, the transaction goes to Missing source.

Important: Transaction dates are not used for matching. Matching is based on IDs and amounts only.

Managing your reconciliations

The main Transaction Reconciliation page lists all your reconciliations. You can filter them by integration, account, date range, and status.

Each reconciliation shows:

• Date range — the period covered
• Integration — which payment platform. Shows Any account if you reconciled an account that isn’t tied to an integration.
• Account — which account was reconciled
• Date created — when the reconciliation was run
• Status — one combined status showing where the reconciliation stands

The status values are:

• In progress — Synder is still building the reconciliation
• Error — the reconciliation couldn’t be completed. Open it to see which step failed and why.
• Attention required — the reconciliation finished, but transactions still need your attention in Discrepancy or Missing source
• Reconciled — nothing is left to resolve

Use the Status filter above the list to narrow what you see. You can select more than one status at a time.

Following a reconciliation as it runs

When you start a reconciliation, Synder shows a process log with the work split into two columns — Accounting and Integration — so you can see how far each side has got: Download source files, Normalize and map, then Match transactions. A Matching rules section at the bottom shows the rules applied. You can reopen the log at any time with the Process log button.

If a step fails, the reconciliation stops there and the log explains why. The error names the file, the row, the column, the value it couldn’t read and the reason — plus how many other rows have the same problem, so you know the size of the fix before you start. You can download the source file straight from the log, correct it, and run the reconciliation again.

Refreshing your results

Sometimes you make changes in your accounting software after running a reconciliation. For example, you might sync missing transactions. In that case, use Refresh data — you’ll find it in the top bar when a reconciliation is open, and in the three-dot menu on the list page. Specifically, it re-downloads only the accounting file without pulling data from the payment platform again. This saves time and replaces your previous results with updated ones.

Deleting and cloning reconciliations

To remove a reconciliation, click the three-dot menu on the list page and select Delete. Deleted items move to the “Deleted” tab, where you can still view results. Furthermore, you can clone a deleted reconciliation. This creates a new one with the same settings pre-filled. If you delete a reconciliation while it is still running, it moves to Deleted with a greyed-out Cancelled status.

Sharing a reconciliation

Click Copy share link in the top bar to copy a direct link to the reconciliation. Anyone you have added to your Synder organization can open that link and land straight on this exact reconciliation.

Exporting results

Click the “Export” button on the results page to download your data. You can export each tab separately — Export matched, Export discrepancy, Export missing source or Export ignored. Alternatively, use “Export all” to get a 4-tab Excel file with all categories.

In addition, you can download normalized and mapped source files from the Process Log.

Limitations & Important Notes

• In Summary mode, reconciliation compares data imported into Synder (not your accounting ledger) against the payment platform. A “Reconciled” result does not confirm the data was correctly synced to your books. If Transaction Reconciliation shows “Reconciled” but you see discrepancies in your accounting software, check that your summaries are synced and your account mapping is correct. If the issue persists, contact Synder support with the specific differences so we can investigate and guide you through the mapping.
• Reconciliation periods cannot overlap for the same clearing account.
• Stripe automation may take up to an hour for large date ranges.
• Synder automatically excludes certain PayPal transaction types, such as Currency Conversion and Account Holds. This prevents false discrepancies.
• For Shopify, reconciliation covers the Shopify Payments clearing account only — not other payment gateways.
• Synder matches based on IDs and amounts only. It does not compare transaction dates.
• For multi-currency accounts, make sure the currency in your payment platform report matches your accounting records.
• You cannot select today’s date for a reconciliation period. The payment platform may not have finalized today’s transactions yet.
• A period is marked as “Reconciled” only when nothing is left unresolved in the Discrepancy and Missing source tabs. Transactions you have ignored count as resolved.

FAQ

Q: How long does Stripe reconciliation take?
A: Anywhere from a few minutes to an hour, depending on transaction volume and date range.

Q: Can I reconcile multiple platforms at once?
A: No. Each reconciliation covers one payment platform and one clearing account. Run them separately.

Q: What do “Missing in accounting” transactions mean?
A: These exist in your payment platform but were not found in your accounting records. Check if they were skipped during sync, excluded by a filter, or fall outside the sync date range.

Q: Can I undo an ignored transaction?
A: Yes. Go to the Ignored tab and un-ignore it. It will move back to its original category.

Q: What if I cannot resolve a discrepancy?
A: If it is non-material, ignore it. If significant, compare the transaction details in both your accounting software and payment platform to find the root cause.

Q: Do I need to map columns manually?
A: Only in Manual mode. For Automated and Assisted modes, Synder assigns column mappings automatically.

Q: Can I save my column mapping for future reconciliations?
A: Yes. When using Manual mode, you can save your mapping as a template and reuse it later for the same integration.

Reach out to the Synder Team via online support chat or email with any questions you have — we are always happy to help you!