Summary Sync Transaction Reconciliation: How to verify data from your platforms in Synder Before You Sync

• How Reconciliation Works
• How to reconcile Stripe transactions (Automated)
• How to reconcile PayPal transactions (Assisted)
• How to reconcile Shopify transactions (Automated)
• How to reconcile other integrations (Manual)
• Understanding your results
• How Synder matches transactions
• Managing your reconciliations
• Limitations & Important Notes

Synder’s Transaction Reconciliation tool helps Summary Sync users verify that the transaction-level data Synder stores matches their payment platform records before summaries sync to the books.

Use this guide if:

• You use Summary Sync and want to validate data before syncing
• You want to catch missing, mismatched, or failed transactions before summaries are created
• You want to confirm that the data inside Synder is complete enough to build accurate summaries

Don’t Use If:

• Using Per-Transaction Sync (use this guide instead)
• You need to reconcile your books, profit and loss, or bank statements inside the accounting platform

Why this matters: Summary Sync creates journal entries in your books from the individual transactions fetched from your platforms. Because the accounting platform does not store those individual transactions one by one, Synder instead compares your payment platform data to its internal transaction-level records.

How Reconciliation Works

Transaction Reconciliation compares:

1. Payment platform data
2. Synder’s transaction-level source data (used for summaries)

Important:

• This workflow validates transactions before they appear on your ledger. In Per Transaction Sync, users usually compare platform records against the transaction-level entries Synder already synced to accounting. However, in Summary Sync, that is not the main use case, because once Synder groups transactions into summary lines, the books no longer keep a clean transaction-by-transaction trail.

• Sync status does not change the reconciliation result. The comparison checks whether the payment platform data matches the transaction-level source data Synder holds. As a result, the answer stays the same whether Synder has already synced the related summary or not.

• The main goal is to detect data gaps before sync. If transactions are missing, mismatched, or failed at the source-data level, you want to catch that before those transactions are grouped into summaries. That gives you time to investigate before the summary is built or synced.

Why Timing Is Critical

Run Transaction Reconciliation before summaries sync. That way, Synder has already validated the data reaching your books.

Pre-sync validation saves time because it helps you avoid rebuilding summaries later and searching for issues after the sync has already happened.

Prerequisites

Before you start, confirm the following:

• Payment platform connected to Synder
• Summary Sync configured
• Know your validation period
• Ideally, the related summaries have not been synced yet

Supported Platforms

How to reconcile Stripe transactions (Automated)

For Stripe, Synder fully automates the reconciliation. Specifically, it downloads both the Stripe 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 “Start reconciling” on the welcome page. Otherwise, click “Add reconciliation” in the top-right corner.
• Next, 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 Stripe as the payment platform.
• Select the clearing account used for Stripe transactions.
• Set the Integration Automation mode to “Automated”.

• Finally, click “Start matching”.
• Synder downloads the Balance Change from Activity report and the Payouts report from Stripe automatically. It also pulls your clearing account details from QuickBooks Online. 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.

How to reconcile PayPal transactions (Assisted)

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

• Go to Transactions → Transaction Reconciliation in the left sidebar.
• Click “Add reconciliation” (or “Start reconciling” 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 clearing account used 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.

• 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 Shopify transactions (Automated)

For Shopify, Synder automates the reconciliation. In addition, it downloads the required Shopify data and your accounting data automatically, so you do not need to upload any report manually.

• Go to Transactions → Transaction Reconciliation in the left sidebar.
• Click “Add reconciliation”.
• Set the date range for the period you want to reconcile.
• Under Accounting, set the Automation mode to “Automated”.
• Under Integration, select Shopify.
• Select the clearing account used for Shopify transactions.
• Set the Integration Automation mode to “Automated”.

• Click “Start matching”.
• Synder will automatically download the Transactions and associated payouts report from Shopify, as well as your clearing account details from QuickBooks Online. This may take a few minutes to an hour, depending on the volume of transactions.
• Review your results once processing is complete.

Important: 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.

How to reconcile other integrations (Manual)

Some integrations do not offer Automated or Assisted modes — for example, Square, WooCommerce, and others. For these, use Manual mode: upload your own CSV or XLSX file and map the columns yourself.

• Go to Transactions → Transaction Reconciliation.
• Click “Add 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. As a result, they are fully reconciled. No action needed.

Moreover, you can expand any matched row to see the individual accounting and integration line items that make up the match, along with their Primary ID, Secondary ID, Transaction type, and Amount.

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.

Not Matched

Synder could not find these transactions in the opposite source. Therefore, the tab splits into two sections:

• Missing in Accounting — transactions that exist in the payment platform but not in your accounting records. For example, Synder may have skipped them during sync, a filter may have excluded them, or they may fall outside your sync date range.
• Missing in Platform — transactions in your accounting records that Synder did not find in the payment platform report.

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

Ignored

These are transactions you manually marked as “ignored.” Generally, use this tab for known or non-material discrepancies. To move items here from the Discrepancy or Not Matched tabs, click “Ignore” or use Bulk-Ignore. If needed, you can un-ignore them later.

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. However, if the totals differ, it goes to Discrepancy. Finally, if Synder finds no match after all three passes, the transaction goes to Not Matched.

Important: Synder does not use transaction dates for matching. Instead, it matches on IDs and amounts only.

Managing your reconciliations

The main Transaction Reconciliation page lists all your reconciliations. In addition, you can filter them by integration, account, date range, matching status, and reconciling status.

Each reconciliation shows:

• Date range — the period covered
• Integration — which payment platform
• Account — which clearing account
• Matching status — Finished, In Progress, Failed, or Cancelled
• Matched % — percentage of transactions that matched
• Reconciling status — Reconciled, Not Reconciled, or N/A

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 the “Refresh data” button. 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.

Exporting results

Click the “Export” button on the results page to download your data. You can export each tab separately (Matched, Discrepancy, Not Matched, or 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 the data Synder imported (not your accounting ledger) against the payment platform. Therefore, a “Reconciled” result does not confirm Synder synced the data correctly to your books. If Transaction Reconciliation shows “Reconciled” but you see discrepancies in your accounting software, first check that your summaries synced and your clearing 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 and Shopify automation may take up to an hour for large date ranges.
• For PayPal and other integrations, you must upload reports manually — Synder does not offer automatic download for these platforms.
• Synder automatically excludes certain PayPal transaction types, such as Currency Conversion and Account Holds. This prevents false discrepancies.
• Synder matches based on IDs and amounts only. In other words, 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.
• Synder marks a period as “Reconciled” only when zero transactions remain in the Discrepancy and Not Matched tabs.

FAQ

Should I run Transaction Reconciliation before or after syncing summaries?

A: Before syncing summaries, whenever possible. That is the safest workflow for Summary Sync users, because it lets you catch missing or mismatched source data before it is grouped into summary lines. If you wait until after sync, fixing the issue becomes more complicated and may require rebuilding, rolling back, or adjusting summaries.

What exactly am I comparing in Summary Sync?

A: You are comparing the payment platform data with the transaction-level source data stored in Synder. This is the data Synder later uses to build summaries. In other words, the tool helps you confirm that the source data inside Synder is complete and accurate before you sync the summary to your books.

If the summary is already synced, can I still use Transaction Reconciliation?

A: Yes, but it is harder to act on the result. Once the summary is already synced, you may need to identify which summary was affected, determine whether more than one summary was impacted, and then decide whether to rebuild it, roll it back, or correct the issue with an adjusting entry.

If I find missing transactions, can I fix them myself?

A: Sometimes you can fix obvious setup issues on your own, such as selecting the wrong date range or uploading the wrong file. However, if the problem is caused by failed, missing, or incomplete source data in Synder, users often need help from Synder Support to investigate and resolve it properly.

Does sync status itself affect the reconciliation result?

A: No. This workflow is a data completeness check, not a sync-status check. In other words, whether Synder has already synced the related summary does not change whether the underlying transaction-level data matches the payment platform data.

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