Navigate to: Reporting > Financial > End of Day Report
Practices typically run this report at the end of each business day, after the last client has checked out. If your practice has multiple staff handling payments throughout the day, the EOD report is also a useful audit tool — the Payments tab records which user processed each transaction.
What This Report Is For
The EOD Report provides an overview of the day's transactions broken down into sections covering invoice activity, payment details, and payment type totals.
Verify daily payment totals — Use the Totals tab to confirm total money collected by payment type at the end of each day.
Review individual transactions — Use the Payments tab to see each payment and refund, who processed it, and which invoice it was applied to.
Reconcile your cash drawer — Use the Cash Reconciliation tab to confirm cash and check totals and prepare your bank deposit.
Monitor refunds — Use the Refunds sub-tab to review all refunds issued during the selected period.
What This Report Is NOT For
Revenue reporting — The EOD report shows what was collected, not what was invoiced. Clients with unpaid balances will appear on invoices but not in payment totals. Use the Summary Report for revenue.
Matching Shepherd Pay batch deposits in real time — The EOD shows all payments applied to invoices — including pending ones. If totals don't match your Shepherd Pay dashboard, the batch likely hasn't closed yet. Voided payments are the only exception — they do not appear in EOD totals.
Tracking failed or attempted transactions — The EOD report only shows payments that were actually collected. Failed or attempted Shepherd Pay transactions appear in the Shepherd Pay Gateway Portal, not here.
Editing or correcting amounts — The EOD report is a read-only view. To correct a discrepancy, fix the underlying payment, invoice, refund, or credit balance in Shepherd — the report will reflect the correction automatically.
What You Need to Know
The EOD Report is organized into four tabs. Each tab reports something different — they are not four views of the same numbers, and they are not designed to match each other directly.
Tab | What it measures | Use it to… |
Invoices | Invoices that had line items added today | Investigate missing or unexpected charges |
Payments | Every payment received and refund issued | Investigate individual transactions |
Cash Reconciliation | Cash and check handling | Prepare your bank deposit |
Totals | Aggregate payment activity by method and net totals | Confirm your daily totals |
For daily reconciliation, start with Totals and Cash Reconciliation
Only use Payments or Invoices to investigate discrepancies.
Credit balance payments and prepayments
Payments made before charges are added to an invoice — such as deposits, prepayments, or credit balance top-ups — appear in the Payments and Totals tabs but not in the Invoices tab. This is expected, and is one of the most common reasons invoice and payment totals differ.
Invoice Date vs. Payment Date
The Invoices tab shows the Invoice Date — when the invoice was created — not when a payment was made. If a payment appears to be on the wrong day, check the Payments tab and look at the Payment Date column instead.
How to Close Out the Day
For most practices, daily reconciliation is just two steps.
Step 1 — Confirm what was collected today
Go to the Totals tab > Payment Total Summary. The Payments Received line is your total money in for the day. The Total line is net after refunds.
Step 2 — Verify your cash and check deposit
Go to the Cash Reconciliation tab > Deposit Summary. This shows your cash and check totals — the exact amounts to bring to the bank.
If something looks off — go to Payments
Open the Payments tab > All Payments to review individual transactions. The User column shows who processed each payment. Check the Refunds sub-tab to review any refunds issued today.
If a charge looks missing or wrong — go to Invoices
Open the Invoices tab and review the Remaining Balance column for unpaid invoices, or look for unexpected line items. Remember: this tab shows invoices with line items added today, not all invoices created or paid today.
Filters
For a complete picture of the day, leave Invoice Status and Payment Method blank.
Applying either filter will exclude activity that doesn't match — and it's easy to accidentally hide payments you're looking for. If you apply an Invoice Status filter, payments not tied to an invoice — such as credit balance top-ups or prepayments — will also be excluded.
Filter | Description |
Time Period (required) | Select Today, Yesterday, or Custom (enter a specific date range). Defaults to Today. |
Invoice Status | Filter results by invoice status: Active, Charges Complete, or Checked Out. Leave blank to show all statuses. |
Payment Method | Filter results to a specific payment method: Cash, Check, Credit Balance, Other, Payroll Deduction, or Sunbit. Leave blank to show all methods. Use this filter to isolate a specific payment type if you need to verify a particular transaction. |
If you change filters after running the report, click View Report again to apply them.
Invoices Tab
The Invoices tab displays invoices that had line items added during the selected time period.
This tab shows invoice activity, not money collected.
The financial columns — Paid, Invoice Total, Daily Total — reflect the state of each invoice as a whole, including payments made on previous days. They will not match the Payments tab totals, and they are not intended to.
To see what was actually collected today, use the Payments tab or the Totals tab.
Which invoices appear here
An invoice appears in this tab when a line item was added to it during the selected time period — not necessarily when the invoice was created. This means:
An invoice created today will appear here if charges were added today.
An invoice created on a previous day will also appear here if additional charges were added to it today.
If a client paid a balance on an older invoice today but no new line items were added to it, that invoice will not appear here — but the payment will still appear in the Payments tab.
This is the most common reason the Invoices tab and Payments tab do not match: a payment toward a historic invoice with no new charges will show in Payments but not here.
Column descriptions:
Column | Description |
Invoice Date | Date the invoice was created. NOT when a payment was made. |
Invoice ID | Unique invoice number; click to open the invoice directly |
Invoice Status | Active, Charges Complete, or Checked Out |
Client ID / Client Full Name | Client identifier and name; click to open the client record |
Patient ID(s) / Patient Name(s) | One or more patients associated with the invoice |
SOAP ID(s) | Associated SOAP record ID(s) |
Subtotal | Charges before tax and discounts |
Tax | Tax applied to the invoice |
Discount | Any discount applied |
Product Return | Value of any returned products + returned item tax |
Daily Total | Total charges billed to this client today across all of their invoices |
Invoice Total | Full invoice amount including all charges, regardless of when they were added — always reflects the complete invoice history, not just today's activity |
Paid | Total amount paid on this invoice to date — this includes payments made on previous days, not only today |
Remaining Balance | Outstanding balance still owed on this invoice. Use this column to identify clients with unpaid balances before closing out the day. |
The row at the bottom shows the total number of invoices and the sum of all Invoice Totals for the displayed invoices — this is a total of charges billed, not payments received.
You can download this tab's data via the Invoices CSV link at the top right of the tab.
Why Daily Total and Invoice Total Can Be Different
Daily Total reflects charges added during the selected period.
Invoice Total reflects the entire invoice value, including charges added on previous dates.
If additional services were added to an invoice across multiple visits or dates, Invoice Total will be larger than Daily Total.
Payments Tab
The Payments tab is divided into two sub-tabs: All Payments and Refunds. This tab is filtered by the Payment Method selected in the filters.
All Payments
Shows all incoming payments received during the selected period, excluding refunds.
Columns included:
Column | Description |
Payment Date | Date and time the payment was recorded |
Payment Type | Card brand or payment method (e.g., Visa, MasterCard, American Express, Discover, Cash, Check) |
Payment ID | Unique transaction identifier |
Last 4 Card No | Last four digits of the card used, if applicable |
Authorization ID | Card processor authorization code |
Amount Paid | Payment amount |
Client ID / Client Full Name | Client associated with the payment; click to open the client record |
Paid Invoice(s) ID | Invoice(s) the payment was applied to; click to open the invoice. Blank if no invoice is associated — this occurs when a payment was applied to a client's credit balance or prepayment rather than directly to an invoice. These payments are still captured here but will not appear in the Invoices tab. |
User | Staff member who recorded the payment |
Outstanding Balance Before Payment | Client’s outstanding balance before last payment recorded up to the selected date |
Outstanding Balance After Payment | Remaining client balance after last payment |
Payment Note | Any note recorded at the time of payment |
The row at the bottom shows the total number of payments and the grand total amount paid.
You can download this tab's data via the All Payments CSV link at the top right of the tab.
Refunds
Shows all refund transactions issued during the selected period. Review this sub-tab daily to catch errors or unauthorized refunds.
Columns included:
Column | Description |
Payment Date | Date and time the refund was issued |
Payment Type | Method used for the refund (e.g., Credit Balance, Debit) |
Payment ID | Unique refund transaction identifier |
Last 4 Card No | Last four digits of the card refunded, if applicable |
Authorization ID | Card processor authorization code for the refund |
Amount Refunded | Refund amount |
Client ID / Client Full Name | Client associated with the refund |
Paid Invoice(s) ID | Invoice(s) the refund was applied to |
User | Staff member who processed the refund |
Outstanding Balance Before Payment | Client’s outstanding balance before last payment recorded up to the selected date |
Outstanding Balance After Payment | Remaining client balance after last payment |
The row at the bottom shows the total amount refunded for the selected period.
You can download this tab's data via the Refunds CSV link at the top right of the tab.
Cash Reconciliation Tab
The Cash Reconciliation tab focuses on cash and check handling. Use this tab to prepare your end-of-day bank deposit. It includes two summaries side by side.
Cash Payment Summary
Tracks all cash that moved through the practice during the selected period.
To export this specific data, click Cash Payment Summary CSV.
Deposit Summary
Breaks down the physical deposit by payment type — the amounts you would bring to the bank.
To export this specific data, click Deposit Summary CSV.
Totals Tab
The Totals tab summarizes all payment activity for the selected period. It includes two summaries side by side.
Payment Type Summary - Shows how payments break down by method.
Payment Total Summary - Shows the net financial outcome for the day.
Cross-reference the Total line against your bank deposit to confirm they align — keeping in mind that non-depositable methods such as credit balance adjustments will not be part of your physical deposit.
To export either summary’s data, click Payment Type Summary CSV or Payment Total Summary CSV.
Frequently Asked Questions
Why doesn't "Paid" on the Invoices tab match "Payments Received" on the Totals tab?
These two numbers measure different things and are not expected to match.
Paid (Invoices tab) shows the total amount paid on each invoice to date — including payments made on previous days. If a client paid a deposit last week and the balance today, both payments are included in the "Paid" figure.
Payments Received (Totals tab) shows only the payments recorded during the selected time period.
There is also a structural reason these tabs can differ: the Invoices tab only shows invoices that had line items added during the selected period. If a client paid a balance on an older invoice today but no new charges were added to it, that payment will appear in the Payments tab but the invoice will not appear in the Invoices tab at all. This is expected behavior.
To see what was actually collected today, use the Totals tab, not the Invoices tab.
Why don't my totals match my deposit?
The most common reasons are:
The Time Period or date range selected doesn't match the period you're reconciling. Make sure the start and end times are correct.
Refunds are subtracted in the Payment Total Summary but may not have been accounted for in your manual deposit calculation.
A Payment Method filter is applied, which is excluding some transactions from the view. Clear all filters and run the report again to see all activity.
You are comparing the wrong tab. Use the Totals tab > Payment Total Summary for your deposit reconciliation number, not the Invoices tab total.
A payment isn't showing up — how do I find it?
Check these common causes in order:
Wrong tab — Switch to the Payments tab. The Invoices tab shows invoice activity, not all payments.
Filters are too narrow — Clear all filters except Time Period and run the report again.
Payment was applied to a prior invoice — The payment may be tied to an invoice from a previous day outside your filter range.
Payment went to credit balance or prepayment — These appear in the Payments tab with a blank Paid Invoice(s) ID column but will not appear in the Invoices tab.
Payment failed or was only attempted — The EOD only shows payments actually collected. Check the Shepherd Pay Gateway Portal for failed attempts.
Why does my EOD report not match my Shepherd Pay batch or bank deposit?
The EOD report reflects payments posted in Shepherd — it does not always match Shepherd Pay batch totals in real time. Common reasons:
Payments are still pending. Shepherd Pay batches may not be complete until after the clinic closes or the following morning.
Failed or attempted transactions appear in the Shepherd Pay Gateway Portal but not in the EOD report.
Refunds and voids may affect same-day or next-day totals differently depending on when they were processed.
If your Shepherd Pay dashboard and EOD report match but the batch report looks incomplete, the remaining payments may simply not have finished batching yet. For the most accurate reconciliation, consider running the EOD report the following morning after all payments have settled.
Does the EOD report include pending payments?
Yes. Payments applied to an invoice will appear in the EOD report regardless of whether the batch has closed. The report reflects the expectation that pending payments will process once the batch closes. The only transactions that will not appear are voided payments, as these do not count toward end-of-day totals.
Why is a backdated payment showing up on an unexpected date?
When a payment is backdated in Shepherd, staff can select the date but not the time — the payment defaults to 12:00 AM on the selected date. If your report uses a time-based range that starts or ends around midnight, a backdated payment may appear outside the range you expect. If a payment seems to be missing or misplaced, check whether it was backdated and adjust your time range accordingly.