QuickBooks Online bookkeeping for Shopify sellers

Your sales are growing.But do you know what you actually keep?

If Shopify, QuickBooks and your bank all show different numbers, I trace the gaps, identify duplicate sales, reconcile payouts, fees and refunds, and give you financials you can actually trust.

QuickBooks Online ProAdvisor Shopify experience Verified 5-star client reviews Email & chat communication
Profit and LossSAMPLE DATA
CustomizeSave customization
Report periodThis month Accounting methodAccrual Display columns byTotal only Run report
Sample Store LLCProfit and LossJune 1 - June 30, 2026
TOTAL
Income
Shopify Sales84,632.18
Discounts-2,184.40
Returns and Refunds-3,041.62
Total Income79,406.16
Cost of Goods Sold
Product Costs31,862.74
Total Cost of Goods Sold31,862.74
Gross Profit47,543.42
Expenses
Advertising15,420.00
Payment Processing Fees2,691.37
Shipping and Fulfillment7,284.60
Software and Operating Expenses5,184.55
Total Expenses30,580.52
Net Income16,962.90
Fictional company and figures created for this sample report.

Your store is making sales, but your financial reports still leave you guessing.

When orders, payouts, refunds, fees and taxes move through different systems, a small setup issue can quietly turn into unreliable revenue, profit and account balances.

$

Revenue is up, but cash is not

Shopify looks healthy while your bank balance tells a very different story.

Payouts do not match deposits

The Shopify payout, bank deposit and QuickBooks entry all show different amounts.

You may have duplicate income

You are not sure whether an app, connector or manual entry recorded the same sale twice.

Fees and refunds look wrong

Processing fees, discounts, refunds, gift cards or sales tax may be sitting in the wrong accounts.

0?

Balances never return to zero

Accounts Receivable, Undeposited Funds or a clearing account keeps carrying an unexplained balance.

?

You cannot explain the reports

Your CPA asks what happened, but the reports do not give you a confident answer.

Are you looking at real profit, or just revenue?

Sales are not the same as profit. Payment fees, refunds, discounts, shipping, advertising, inventory costs and sales tax all affect what your business actually keeps. You do not need another report full of numbers. You need Shopify, QuickBooks and your bank to tell the same financial story.

Find out what is distorting your numbers before you pay for a full cleanup.

The QuickBooks Health Check is for e-commerce owners who know something feels wrong, but need a clear diagnosis before deciding what to fix.

Start here if you are asking:

Is my income duplicated? Are Shopify payouts complete? Are fees, refunds and sales tax recorded correctly? Can I trust my profit?

Start with a Health Check

What you receive from the review

Clear, usable findings
01

Findings Summary

A plain-English explanation of what looks wrong, where the risk sits and why it matters.

02

Payout Review

A focused check of how Shopify payouts, bank deposits and QuickBooks activity connect.

03

Profit Snapshot Review

A review of the P&L areas most likely to be distorted by sales, refunds, fees or mapping issues.

04

“Fix First” Action Plan

Prioritized next steps, so you know what needs attention now and what can wait.

The Health Check identifies and documents the issues. Any cleanup work is scoped separately after the findings are reviewed.

How healthy are your e-commerce books?

Answer five practical questions to see whether your current workflow shows warning signs worth reviewing.

This is a general screening tool, not an accounting opinion or formal diagnosis.
Do Shopify payouts consistently match the related bank deposits?
Can you explain your monthly profit after refunds, fees and other store costs?
Are Shopify sales recorded in QuickBooks through one clearly defined workflow?
Are old Accounts Receivable, Undeposited Funds and clearing balances explained?
Would you feel confident explaining your P&L and Balance Sheet to your CPA?
Your answers stay on this page.

Start with clarity. Fix what is wrong. Keep it right every month.

01

QuickBooks Health Check

For owners who know something is wrong but do not yet know where the problem begins.

  • Duplicate income and unusual balance review
  • Payout, refund and tax risk check
  • Prioritized findings and action plan
Best first step
02

Shopify + QuickBooks Cleanup

For businesses with historical duplicates, open balances, incorrect mappings or unreliable reports.

  • Documented corrections
  • Key account reconciliation
  • Future workflow recommendations
Fixed scope after review
03

Monthly E-commerce Bookkeeping

For owners who want Shopify payouts, fees, refunds, bank activity and QuickBooks aligned every month.

  • Monthly reconciliations
  • P&L and Balance Sheet review
  • Clear summary of unusual items
Ongoing support

The connector is part of the bookkeeping system, not just a technical setting.

I review how Shopify activity is configured to reach QuickBooks, because customer settings, refunds, product mapping and deposit accounts can directly affect the financial reports.

  • Order and refund workflow
  • Customer and product mapping
  • Deposit and clearing account setup
  • Sync warnings and exceptions
Anonymized Shopify to QuickBooks Online connector configuration reviewed during client work
Real connector workflow screen from client work. Client identity has been redacted.
Not sure where to start? The Health Check defines the problem before you commit to a cleanup.Get clarity on my books

The goal is not more bookkeeping. It is numbers you can explain and use.

Every project begins by understanding how sales, payments, refunds, fees and deposits move through your systems, then documenting what needs to change.

BeforeAfter
01
Shopify, the bank and QuickBooks show different totals.
The gaps are traced and grouped by cause.
02
You suspect duplicate income but do not know where it entered.
The sales workflow is reviewed and the duplicate risk is documented.
03
Payouts, fees and refunds are difficult to follow.
The movement between orders, payouts, deposits and QuickBooks is easier to verify.
04
You do not know whether you need a small correction or a full cleanup.
You receive a prioritized plan and a clearer scope for the next step.

Complex bookkeeping problems, translated into a clear correction plan.

01

Shopify and QuickBooks historical cleanup

The problem

Overlapping sync workflows created duplicate sales activity, old open invoices and balances that no longer told a reliable story.

What I reviewed

Orders, payments, refunds, Accounts Receivable, clearing accounts, sales tax and connector settings.

The outcome

Duplicate activity was identified, open invoices were resolved and historical activity was separated from the correct future workflow.

02

Connector and sales tax diagnostic

The problem

Online orders, draft orders and refunds were not reaching QuickBooks with consistent tax treatment.

What I reviewed

Tax codes, product settings, refunds, payout posting, item mapping and the Shopify to QuickBooks workflow.

The outcome

The client received a documented diagnosis, specific examples and a prioritized correction plan.

03

Accounting vs operations reconciliation

The problem

Sales totals in the operating system and QuickBooks did not agree, making monthly reporting difficult to trust.

What I reviewed

Transaction-level exports, credits, refunds, timing differences, missing entries and duplicate activity.

The outcome

A repeatable review grouped every difference by type and preserved the supporting evidence for verification.

What clients say about working together.

Verified client reviews
★★★★★
“Had a great experience, everything is very detailed and now onto the next step!”
visionsaddlery - CanadaQuickBooks Health Check · Fiverr client
★★★★★
“Two great experiences! I highly recommend!”
visionsaddlery - CanadaMonthly Shopify Bookkeeping · Repeat client
★★★★★
“Best bookkeeper alive.”
john_web3 - FranceNotion Finance Setup · Fiverr client
★★★★★
“The Health Check breaks everything into bite-size tasks with pre-built Notion views and straight ‘Fix next’ notes. I matched Orders vs Payouts, mapped processor fees correctly, did a quick sales-tax sanity check, and finished with a clean Profit snapshot (mini KPI view). I uncovered a fee gap I wasn’t tracking and set a 20 minute weekly close. Definitely beginner friendly but precise.”
Daniela - United States7-Day E-commerce Health Check · Etsy customer
Tijana, e-commerce bookkeeper and QuickBooks Online ProAdvisor

Detail-oriented work, explained like a human.

I am a certified QuickBooks Online ProAdvisor specializing in bookkeeping and cleanup for Shopify and e-commerce businesses. I combine detailed financial review with clear, practical communication, so you understand what was found, why it matters and what should happen next.

I work remotely with international clients and keep important findings documented through organized email and chat communication.

QuickBooks Online ProAdvisorCertified knowledge of QBO workflows and controls
Intuit Bookkeeping CertificateFormal bookkeeping foundation and reporting knowledge
Hands-on e-commerce experienceShopify, payouts, sales tax, clearing and connector diagnostics

More than transaction categorization

E-commerce bookkeeping is about understanding how orders, payments, refunds, fees, taxes and payouts move between systems.

  • I investigate why numbers do not match
  • I document what was found and changed
  • I avoid unsupported corrections
  • I understand Shopify connector workflows
  • I communicate clearly by email and chat
  • I build a process that can be repeated

Know what to expect before sharing access.

The goal is to confirm the problem and scope first, then request only the information needed for the agreed work.

Can you review my books before I commit to a full cleanup?

Yes. The QuickBooks Health Check is designed to identify the main issues and determine the correct scope before any cleanup begins.

Can you fix duplicate Shopify sales in QuickBooks?

In many cases, yes. I first identify how the duplicate activity was created, confirm which transactions are valid and prepare a documented correction plan.

Do you work with Shopify connectors?

Yes. I review how orders, payments, refunds, taxes and payouts are mapped between Shopify and QuickBooks.

Will you file my taxes?

No. I provide bookkeeping cleanup, reconciliation and financial reporting. Your cleaned financials can then be provided to your CPA or tax professional.

Do I need to give you access immediately?

No. We first confirm the scope and required reports. Access is requested only when it is necessary for the agreed work.

What feels messy right now?

Tell me what does not match, what you are unsure about or what your accountant has questioned. I will help you determine whether you need a Health Check, a focused cleanup or ongoing bookkeeping.

  • Nothing is sent until you press Send
  • No access required at this stage
  • Clear next-step recommendation
View my verified Fiverr profile →

Get clarity on your books.

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Last updated: July 22, 2026

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