How to Import Accountant Changes in QuickBooks Desktop

Accountant changes in QuickBooks Desktop are not optional. These are adjustments your accountant makes in a copy of your company file to correct reconciliation gaps, fee allocations, tax mapping, and more.

When you ignore or mishandle these changes, you are choosing to keep known errors in your books, errors that can snowball into bigger problems every month. 

This guide shows you how to import accountant changes in QuickBooks Desktop safely, collaborate effectively, and leverage automation to minimize corrections.

The real cost of skipping accountant updates

The consequences of skipping updates are real:

• Audit risk: Your books may not match bank deposits or settlement reports, increasing the chance of audit failures and compliance penalties
• Financial decision errors: Unreconciled payouts and misallocated fees can inflate margins by 3–5 percent, leading to poor inventory and pricing decisions
• Inefficient closes: Each delay adds days to your month-end close, multiplying manual work and correction cycles
• Wasted time: Companies averaging 500 orders per month waste over 40 hours on corrections if changes are not imported promptly

PartyMachines, a multichannel retailer, spent weeks on manual reconciliation before automating its workflow. The result was a $15,000 tax adjustment that could have been avoided with timely accountant imports and automation.

5 types of corrections your accountant makes (and why)

Before we delve into how to import accountant changes in QuickBooks Desktop, note that most accountant changes fix upstream data issues: payout timing, fee allocation, returns, tax mapping, and inventory adjustments. 

Accountant changes in QuickBooks Desktop are adjustments your accountant makes in a copy of your file, sent back for import. Each correction addresses a specific gap in your accounting workflow. 

Here are the five most common types:

1. Payout reconciliation timing

• The issue: Marketplaces like Amazon and Shopify settle payments 7–14 days after orders ship. Your books may show revenue when orders are fulfilled, but cash arrives later with fees deducted.
• The correction: Your accountant aligns revenue recognition with actual cash received, preventing inflated cash flow reports.
• Business impact: A $50,000 monthly seller could show $7,000 in phantom revenue without proper reconciliation. This leads to overstated margins and inaccurate financial reports.

2. Fee allocation errors

• The issue: Marketplace commissions and payment processor fees often arrive as lump sums, not itemized by order. These fees may post to generic accounts instead of the correct expense categories.
• The correction: Your accountant breaks apart bundled fees and allocates them to the right accounts, Amazon fees to one, payment processing to another.
• Business impact: Misallocated fees can inflate margins by 2–5 percent and obscure true channel profitability.

3. Returns and refund gaps

• The issue: Refunds are processed days after the original order, sometimes through different systems. This creates orphaned credits without matching invoices.
• The correction: Your accountant posts credit memos and adjusts inventory, ensuring refunds offset original revenue properly.
• Business impact: Missed refunds mean overstated revenue and incorrect inventory valuations.

4. Sales tax mapping

• The issue: Multi-state sellers face different tax rules by jurisdiction. Orders may be tagged with the wrong tax codes or rates.
• The correction: Your accountant fixes tax mappings and adjusts for nexus rules, ensuring compliance across states.
• Business impact: Incorrect tax postings lead to audit exposure and potential penalties.

5. COGS and inventory adjustments

• The issue: Physical counts often do not match system records. Damaged goods, samples, and shrinkage create discrepancies.
• The correction: Your accountant adjusts the cost of goods sold (COGS) to reflect actual inventory movement and write-offs.
• Business impact: Overstated inventory inflates assets and distorts profitability metrics.

Automation tools like Webgility can reduce the frequency of these corrections by syncing orders, payouts, and fees in real time. 

Suggested Read: QuickBooks Online vs. Desktop

Common pitfalls and how to prevent them

The most important headaches can be prevented by addressing root causes before the accountant’s copy is created. 

Here are the most common pitfalls, their root causes, and how to prevent them:

Table: Common Accountant Import Pitfalls

Pre-import checklist:

• Backup your QuickBooks file
• Confirm you have the correct company file open
• Review proposed changes before accepting

Channie’s, a Webgility customer, cut correction cycles and manual errors by over 80 percent after automating order and payout sync. 

Step-by-step: How to import accountant changes in QuickBooks Desktop

Follow these steps to safely import accountant changes and keep your books accurate:

1. Backup your QuickBooks file: Before starting, create a full backup of your company file. Go to File > Back Up Company > Create Local Backup. Store the backup in a secure location.
2. Receive the accountant’s copy: Your accountant will send you a file, usually with a .QBY extension. This file contains the changes made in your accountant’s copy.
3. Open QuickBooks Desktop and navigate to the import tool: Open your company file in QuickBooks Desktop. Go to File > Send Company File > Accountant’s Copy > Client Activities > Import Accountant’s Changes from File.
4. Review proposed changes: QuickBooks will display a summary of all changes. Review each line item to ensure it matches your expectations. If you see anything unexpected, pause and consult your accountant.
5. Resolve conflicts: If both you and your accountant made changes to the same transaction, QuickBooks will flag a conflict. Decide whether to accept your accountant’s change or keep your own. When in doubt, consult your accountant.
6. Accept or reject changes: Once you have reviewed and resolved any conflicts, accept the changes to update your company file. If you reject the changes, no updates will be made.
7. Confirm import success: Check for error messages and verify that changes appear in your reports. If something looks off, restore your backup and contact your accountant.

Pre-import checklist:

• Backup created
• Correct file open
• Changes reviewed

Teams using automation tools like Webgility often find fewer corrections are needed at this stage, as data is already up to date. 

Best practices for collaborating with your accountant

The most efficient teams combine data hygiene, clear communication, and automation to minimize back-and-forth.

Data hygiene checklist before sending the accountant’s copy

• All orders posted
• Refunds and returns recorded
• Tax codes mapped
• Fees and payouts synced

Collaboration tactics

• Set a regular review schedule (weekly or monthly)
• Use QuickBooks notes to provide context for changes
• Flag unusual adjustments for discussion
• Confirm changes align with business reality

When to involve your accountant vs. automate

• Routine order, payout, and fee sync: Use automation
• Strategic adjustments (tax planning, complex reconciliations): Involve your accountant

Vector Business Solutions, a Webgility customer, enabled cleaner handoffs and reduced correction cycles by 90 percent after automating their workflow. 

When to automate vs. when to call your accountant

Modern teams combine real-time automation with accountant insight for scalable, error-free workflows.

• Real-time automation: Tools like Webgility auto-sync orders, payouts, and fees, reducing manual corrections and keeping your books up to date.
• Multi-channel and multi-location sync: For businesses with multiple stores or channels, automation ensures consistency and centralization across all data sources.
• Scheduled syncs and exception handling: Set up automation to run on a schedule and flag exceptions for manual review, so nothing slips through the cracks.
• What accountants still do: Strategic adjustments, complex reconciliations, and tax planning require professional expertise.

Table: Manual vs. Automated Workflow Comparison

Your path to audit-ready books

Importing accountant changes is essential, but modern teams combine this with automation for true efficiency. 

Consistent, careful importing plus automation delivers cleaner books and faster closes. By reducing manual corrections, you gain:

• Cleaner, more accurate books
• Faster month-end closes
• Fewer manual corrections and errors

Assess where automation can reduce your manual corrections. Webgility customers have often saved up to 90 percent of reconciliation time and closed their books 3x faster. 

Ready to streamline your workflow? Get a demo and see how automation can support your team.

FAQs

What is an accountant’s copy in QuickBooks Desktop?

An accountant’s copy is a special version of your company file that lets your accountant make changes while you keep working. When finished, your accountant sends you a file with their changes for import.

How do I resolve conflicts when importing changes?

QuickBooks flags any conflicts between your changes and your accountant’s. Review each conflict and decide whether to accept your accountant’s change or keep your own. If unsure, check with your accountant.

Can automation eliminate the need for accountant changes entirely?

Automation can reduce the frequency of corrections by syncing orders, payouts, and fees in real time. However, strategic adjustments and complex reconciliations still require an accountant’s expertise.

How does automation help with QuickBooks Desktop imports?

Automation tools sync your ecommerce and accounting data, reducing manual corrections and making the import process smoother and faster.