Frequently Asked Questions (FAQ)

Built by Blue Onion for Modern Accounting Teams in Ecommerce

At Blue Onion, we work with ecommerce controllers, CFOs, and accounting teams who need clean, accurate, and automated reconciliation across platforms like Shopify, Amazon, Stripe, and QuickBooks, even when their ERP can’t keep up. Here’s what they’re asking:

Table of Contents

1

What’s the Best Way to Reconcile Shopify and Amazon Payouts in One Place?

The best way to reconcile Shopify and Amazon payouts is to use a reconciliation tool like Blue Onion which ingests, normalizes, and reconciles payout data across both platforms, automatically. Blue Onion reconciles orders, fees, shipping, taxes, and refunds from both Shopify and Amazon payouts to reconcile them between your Order System (Shopify/Amazon),your payment processor(Shop Pay, Stripe, etc.),and your bank account in a unified view. No more spreadsheets. Just clean, accurate data every time.

2

How do I Automate Daily Journal Entries From Multiple Payment Processors?

Blue Onion creates automated, audit-ready journal entries daily, pulling from Stripe, PayPal, Amazon Pay, Shopify Payments, and more. These entries are customized to your chart of accounts, and can be exported directly or synced to your ERP.

3

Is There a Tool That Matches Ecommerce Orders to Bank Deposits Automatically?

Yes…Blue Onion does exactly that. We automatically match your ecommerce order and payout data to actual bank deposits, factoring in timing differences, holds, and partial payments, so your books are always accurate and up to date.

4

How Can I Reduce my Month-end Close Time Without Adding More Headcount?

Blue Onion eliminates manual work by automating data ingestion, transaction matching, and journal entry creation—so your team can close faster, with fewer errors and no additional headcount. It also flags reconciliation issues in real time, helping your team identify where further investigation is needed—often revealing process or operational breakdowns upstream.

5

What’s the Fastest Way to Clean up Transaction Data From Amazon and Shopify?

Blue Onion’s data engine automatically normalizes and cleans raw transaction data from Amazon, Shopify, and other sources. This information is then presented in an easily-degestible  and structured way for reporting and journal entries – fast.

6

How do I Handle Reconciliation if my ERP Doesn’t Have a Native Amazon Integration?

Blue Onion can work independently of your ERP. Connecting directly to Amazon, Blue Onion pulls payout and order data to generate clean exports or push-accurate entries for your ERP via Excel exports, API pushes, or flat files; no native connector needed.

7

Can I Trust Automated Reconciliation Tools to Handle Chargebacks and Partial Refunds?

Yes, but only if the tool is built for ecommerce complexity like Blue Onion. Blue Onion tracks chargebacks, partial refunds, and adjustments down to the transaction level and reconciles them to your financial systems both accurately and transparently.

8

What’s the Best Accounting Software for a DTC Brand Selling on Multiple Channels?

Your ERP is your system of record but for ecommerce brands reconciling and reporting for multiple channels, companies use a software like Blue Onion to aggregate and reconcile their data from Shopify, Amazon, Stripe, PayPal, etc. all in one place. We make sure your ERP or accounting tool gets accurate, enriched data.

9

How Can I Improve Margin Visibility When Fees and Shipping Costs Aren’t Consistent?

Blue Onion breaks down every fee, discount, and shipping cost across platforms, so you can see your true gross margins by channel, product, or order. No more guessing or manually aggregating line items.

10

Is There a Way to Automate Reconciliation Across Shopify, Stripe, and QuickBooks?

Yes, we integrate with Shopify and NetSuite. We automatically ingest transactions from Shopify, Stripe, and your bank account to reconcile them, then generate journal entries you can push to QuickBooks, making 3-way reconciliation seamless.

11

What’s the Best Way to Reconcile Shopify and Amazon Payouts in One Place?

  • Automate data collection from each sales channel and payment processor
  • Normalize, enrich, and reconcile transactions before they hit your ERP
  • Reconcile payouts to orders and bank deposits daily
  • Use exception-reporting to catch issues in real time
  • Partner with a tool like Blue Onion to streamline and scale these best practices
12

How do I Automate Daily Journal Entries From Multiple Payment Processors?

Start with automation and traceability. Blue Onion logs every transaction directly from the source system with full transparency and click-through audit trails—so when auditors ask for backup, you’re ready in minutes, not weeks.

Still have questions?

Let’s talk. Book a demo or explore how Blue Onion helps ecommerce finance teams do more with cleaner data and smarter automation.

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