Stripe Shopify PayPal Payouts, Solved

Stripe, Shopify, and PayPal rarely hand you deposits that match the sales totals you see on your dashboard. Fees are netted out. Refunds and chargebacks hit later. Sales tax gets mixed into payouts. If you post everything directly from your bank feed, you will almost certainly double-count revenue, miss fees, and distort your margins. This guide gives you a clear, repeatable way to post gross sales, fees, refunds, disputes, and sales tax so your books tie to the penny. You will set up clearing accounts, use daily summaries, and create smart bank-feed rules that keep payouts clean without double-counting.

Why Payouts Rarely Match Sales

Each order flows through multiple systems. Shopify records the sale. A payment processor like Stripe, Shopify Payments, or PayPal collects the money, deducts fees, and sends you a payout later. Refunds and chargebacks often settle on different days than the original sale. That timing gap is the root of reconciliation problems. Stripe’s own reconciliation guide calls out the need to account for time lags, fees, refunds, and disputes, and to match against bank statements on a regular cadence using automation where possible. See Stripe’s overview of reconciliation best practices: Ecommerce payment reconciliation 101.

Key Terms You Must Track

Start by defining what should appear in your books. Gross sales are the total value of orders at checkout before any fees. Net sales are gross sales minus returns, discounts, and allowances. Sales tax collected is a liability you hold until it is remitted to a tax authority. Payment processing fees are the Stripe or PayPal costs pulled from your payouts. Refunds are amounts returned to customers and should reverse the related revenue and sales tax. Chargebacks are disputed card transactions with a separate fee and a resolution process. Shopify explains how to collect evidence and track outcomes: Chargebacks and inquiries.

Set Up Your Chart of Accounts

Clean reconciliation starts with the right accounts. Create revenue, contra, fee, tax, and clearing accounts that mirror how money flows.

Revenue and contra accounts

Sales Revenue: Main product sales. Use separate accounts if you also sell services or shipping.

Sales Discounts and Returns: Contra revenue accounts for refunds and discounts so you can track rates cleanly.

Tax and fee accounts

Sales Tax Payable: Liability for tax collected on orders.

Stripe Fees, PayPal Fees, Shopify Payments Fees: Separate expense accounts per processor.

Chargeback Fees: Separate from processing fees to monitor dispute costs.

Clearing accounts

Stripe Clearing, PayPal Clearing, Shopify Payments Clearing: One asset account per processor. These act as temporary holding ledgers between sales and bank deposits. They should trend toward zero after payouts post.

Clearing Accounts and Daily Summaries

The most reliable approach uses daily summary journal entries and clearing accounts. Bookkeep.com popularized this structure to prevent duplicate revenue when the same order shows up in both a platform and a processor. Their recommendation is to post sales to clearing, post fees and adjustments to clearing, then post bank deposits that clear it down. See their guide: How to avoid double booking revenues.

In practice, you post one daily sales summary per channel, splitting the tenders into the right clearing accounts. Then post processor activity that reduces those clearing balances for fees, refunds, and chargebacks. Finally, match the bank deposit to the clearing account. The clearing balance should always reflect money in transit and reconcile to your expected payout reports.

Posting Daily Shopify Activity

Shopify is your source of truth for what was sold, tax collected, discounts, and refunds initiated. For each day, download or run a summary that shows gross sales, discounts, returns, shipping income, tax, and tender types. If you use Shopify Payments, those orders will settle through Shopify Payments Clearing. If a customer chooses PayPal at checkout, the cash will ultimately arrive via PayPal Clearing even though the order originated in Shopify.

Post a single daily entry that credits Sales Revenue for gross sales and Shipping Income if you track it separately, credits Sales Tax Payable for tax collected, and debits each processor clearing account by the funds expected to be collected by that processor for that day’s orders. Use contra accounts for discounts and returns so you can track their rates over time. This keeps one clean revenue entry per sale without duplication.

Posting Stripe and PayPal Activity

Processors have the definitive record of their fees, holds, and adjustments. Stripe and PayPal reports show the exact fees per payout, as well as any chargebacks and refunds that were settled that day. For each processor, post a daily or payout-level entry that debits Fees Expense and credits the respective Clearing account. If a refund or chargeback is processed by the gateway, reduce the clearing account and post the offset to Refunds or Chargebacks. Accounting Atelier’s guide for ecommerce sellers stresses reconciling gross versus net to avoid overstated revenue and calls out clearing accounts as the simplest way to see what is truly collected: Ecommerce bookkeeping guide.

Refunds, Disputes, Chargebacks

Refunds initiated in Shopify reduce revenue and sales tax payable. If your processor deducts refunds from a later payout, record the refund on the day it is processed by the gateway and hit the correct clearing account so the payout nets correctly.

Chargebacks follow a separate timeline. When notified, record a chargeback receivable or post directly to Chargeback Expense with a credit to the processor clearing account for the disputed amount. When the dispute is resolved, reverse the entry accordingly. Track chargeback fees in a dedicated expense account. Shopify’s help center explains timelines and the evidence process: Chargeback process. Keeping the accounting separate for refunds and chargebacks helps you see customer service trends versus fraud or payment issues.

Matching Bank Deposits

Bank deposits should never hit Sales Revenue directly. Each Stripe, Shopify Payments, or PayPal deposit should be matched against its clearing account. Stripe’s best practices call for reconciling to the bank, accounting for timing differences, and using automation where possible. For example, a Stripe deposit of 9,420.50 is recorded as a debit to your bank and a credit to Stripe Clearing for the exact amount of that payout. If the clearing balance does not net to zero after posting fees and the deposit, you are missing an item such as a refund, a dispute, or a transfer fee.

If PayPal holds funds or releases partial payouts, your PayPal Clearing account should show a positive balance equal to funds still pending. When the hold releases and hits the bank, the clearing account reduces accordingly.

Avoiding Double-Counting

The most common mistake happens when sellers post Shopify sales as revenue and then also post PayPal payouts as revenue. That books the same order twice. The cure is structural. Post revenue once from your order system and route the cash side into clearing accounts by tender. Then post processor fees and activity against those clearing accounts. Finally, post bank deposits to those same clearing accounts. Bookkeep.com’s method sums this up: one set of sales entries, one set of processor entries, one set of bank entries. No payout should ever post to Sales Revenue directly. See details: Avoid double booking revenues.

Sample Daily Summary

Consider one day of Shopify orders where customers paid via Stripe and PayPal.

Component and Amount

Gross Sales: 1,000.00

Discounts: (30.00)

Net Sales: 970.00

Sales Tax Collected: 70.00

Total Tendered: 1,040.00

Tender Breakdown Stripe: 800.00

Tender Breakdown PayPal: 240.00

Daily Shopify sales entry

Debit Stripe Clearing 800.00

Debit PayPal Clearing 240.00

Credit Sales Revenue 970.00

Credit Sales Tax Payable 70.00

Credit Discounts and Returns 0.00 if not broken out above, otherwise reflect the 30.00 as a debit to Discounts and a credit within Sales Revenue presentation per your policy.

Later, Stripe reports a 2.9% plus 0.30 fee structure and the payout arrives net of 3.20 in fees for this day’s charges. PayPal shows 7.20 in fees for its portion.

Processor entries

Debit Stripe Fees 3.20

Credit Stripe Clearing 3.20

Debit PayPal Fees 7.20

Credit PayPal Clearing 7.20

Bank deposits

Debit Bank 796.80

Credit Stripe Clearing 796.80

Debit Bank 232.80

Credit PayPal Clearing 232.80

After these entries, Stripe Clearing equals zero and PayPal Clearing equals zero. Your sales, tax, and fees are all stated explicitly.

Refunds and Chargeback Example

Suppose the next day you process a 100.00 refund for a Stripe customer, including 7.00 of sales tax. Stripe nets this refund from your next payout and does not return the original processing fee.

Entry when the refund is processed by Stripe

Debit Sales Returns 93.00

Debit Sales Tax Payable 7.00

Credit Stripe Clearing 100.00

If Stripe also charges a 15.00 dispute fee on a separate chargeback that same day

Debit Chargeback Fees 15.00

Credit Stripe Clearing 15.00

The next payout will be lower by 115.00. Your clearing account captures that and keeps your bank reconciliation clean.

Automate With Bank Rules

Automation reduces errors and saves time. Stripe recommends using platform reports and system integrations to document, summarize, and automate reconciliation. See Stripe’s reconciliation guidance. In QuickBooks Online or Xero, create bank rules that identify deposits from Stripe, Shopify Payments, and PayPal by bank description and automatically code them to the corresponding clearing account, not to revenue; map processor fee withdrawals or negative deposits to the correct fees expense account and clearing account; and match transfers between processors and your operating account so they do not inflate revenue.

Consider middleware that posts daily summaries and fee entries automatically. Tools like Bookkeep, webhooks, or iPaaS platforms can push entries that mirror the three-step flow described above.

Month-End Checks

Close the month with a short checklist.

Clearing balances: Each clearing account should equal the pending payouts shown on your processor dashboards at month end.

Sales tax: Sum tax collected in your entries and compare to your tax platform or Shopify tax reports.

Fees as a percentage: Track processor fees divided by gross sales.

Returns and chargeback rates: Review the rate against net sales.

Payout timing: Confirm cutoff dates for processor payouts so your clearing balances make sense across month end.

Common Mistakes to Avoid

• Posting deposits to Sales Revenue.

• Recording the same Shopify sale again when PayPal pays out.

• Ignoring timing lags.

• Combining all fees into one bucket.

• Letting clearing accounts drift.

When Shopify and PayPal Mix

If Shopify captures orders and customers pay with PayPal, you will see the order in Shopify and the cash in PayPal. If you post both systems’ sales reports to revenue, you double-count. The fix is to treat Shopify as the sales source and PayPal as a bank-like processor. Post the daily Shopify sales entry to PayPal Clearing for PayPal-tendered orders. Then post PayPal’s fees and the bank deposit against PayPal Clearing. Review details: Inter-app clearing approach.

Handling Payout Lags and Holds

Stripe, Shopify Payments, and PayPal have different payout schedules and may hold funds. Your clearing accounts should mirror those holds. If PayPal holds 2,000 for reserve, your PayPal Clearing balance should include that amount until it is released. If Stripe short-pays a deposit due to a chargeback, the difference should already be captured by entries that credit Stripe Clearing for the dispute and fee. Stripe’s guide highlights the need to document every transaction so you can trace a bank deposit back to the original charges and adjustments.

Simple Implementation Plan

Day 1: Add separate fee expense accounts and one clearing account per processor. Lock in your revenue and contra accounts.

Day 2: Set up daily Shopify sales summary reports broken out by tender type. Identify how you will fetch Stripe and PayPal fee and payout reports.

Day 3: Post entries for the last seven days manually to test the flow. Confirm that clearing accounts net to zero after deposits.

Day 4: Add bank rules to auto-code deposits to clearing accounts and fees to the correct expense accounts.

Day 5: Evaluate automation.

FAQ

What if one payout covers multiple days?

Post a daily sales entry to clearing for each day. When the payout arrives, credit the clearing account for the total deposit. The remaining clearing balance should equal the portion of sales that will hit in the next payout.

What if a refund processed after month end relates to last month’s sale?

Record the refund on the date the processor settled it. Consider a month-end adjustment for material post-period refunds if you report on an accrual basis.

How do I handle multicurrency payouts?

Create a separate clearing account per currency per processor. Record sales in functional currency and post realized gains or losses when the payout converts.

Should I use Undeposited Funds instead of clearing accounts?

Undeposited Funds suits grouping checks or cash. For ecommerce, dedicated clearing accounts per processor give better visibility.

Where do I record shipping charged to customers?

Record it as Shipping Income in your daily sales entry. Record carrier bills as Shipping Expense.

How do I book gift cards?

When sold, credit a Gift Card Liability and debit the appropriate clearing account. When redeemed, reduce the liability and recognize revenue.

What if my clearing account will not zero?

Trace the difference using processor payout reports. Common causes are missing fee entries, refunds processed after the sales entry, or disputes not posted.

What changes if I use Shopify Payments instead of Stripe?

Treat Shopify Payments as its own processor. Create a Shopify Payments Clearing account and apply the same three-step structure.

Resources:

Stripe on reconciliation patterns and timing differences: Ecommerce payment reconciliation 101

Bookkeep on avoiding duplicate revenue and inter-app clearing: How to avoid double booking revenues

Shopify on chargebacks and timelines: Chargeback process

Accounting Atelier on gross versus net and clearing accounts: Ecommerce bookkeeping guide