The Integration Problem: Why Your Accounting Software Doesn’t Sync the Way It Should

The sync problem in accounting software refers to the difficulty or failure of different systems (such as accounting platforms, CRMs, ERPs, or payment processors) to share data accurately with each other. This often results in incomplete, delayed, or mismatched financial records.

If accounting systems could talk, half of them would probably say, “You’re asking me to sync with what now?” And honestly, that’s not far from the truth! Studies show that about 26% of accounting software users have reported data loss, and 21% have expressed concerns about additional costs due to sync or integration problems. 

Initially, many small D2C companies and consumer brands start with limited and simple tools. But as they grow, the “software stack” becomes a tangled web of multiple:

• Sales channels
• Inventory tools
• ERPs
• CRMs
• Payment apps, and more

Usually, such finance systems are highly fragile, with one mismatch or missing field being enough to break the entire chain. Don’t want that? Read this article to learn why these accounting problems happen, how they impact your daily operations, and the steps you can take to resolve them before they drain time and money.

Why Accounting Software Sync Breaks?

A 2025 survey found that about 53% of financial services leaders struggle because their data is scattered across different systems that do not connect. But why? That’s largely because when information stays trapped in separate software, teams cannot share or sync data across platforms. 

This creates accounting problems, delays, and errors in financial reporting and daily operations. The survey also shows that removing these “data silos” has now become a major priority for several D2C companies and consumer brands in 2025. 

But why do such sync-related accounting problems occur? Let’s check out some common reasons: 

1. When Two Systems “Speak Different Languages”

Different software follows its own rules for storing and showing data. So, when you try to sync them, the information does not always line up. For example, 

• Your CRM may let you save multiple addresses for one customer
• But your accounting tool may accept only one. 
• Now, when both systems try to match this data, they struggle to decide which address is correct. 
• The impact? It leads to:
  • Missing entries
  • Duplicate customers
  • Wrong information is showing up in your books

Okay, so what’s the core problem here? The two tools were never designed to structure data in the same way, so they fail to interpret each other’s details during sync.

2. Wrong Field Mapping During Setup

Before two systems can exchange data, each field in one system must be linked to the correct field in the other. If this setup is wrong, the sync falls apart and leads to accounting problems. For example, 

• Let’s say a payment type in your sales system may not match the payment type list in your accounting tool. 

or

• A tax code in one system may point to a different tax rule in the other. 

When these mismatches occur, the accounting software does not know where to place the incoming data. As a result, entries may land in the wrong accounts or show incorrect tax amounts. Be aware that these issues usually arise when the initial configuration is done with negligence.

3. Weak Internet or Software Glitches Break the Sync

Syncing requires a steady internet connection! That’s because the systems send information back and forth in real time. Now, if the connection drops, even for a moment, the transfer may stop halfway.

This leads to:

• Creation of half-saved transactions
• Missing updates
• Duplicate entries when the system tries again

On top of that, software bugs in either platform can block the sync even if your internet is fine. These glitches may show up after updates, during heavy system load, or when the software encounters data it cannot process.

4. Missing Permissions Can Stop the Sync Midway

Every accounting or business tool controls what each user can do through permissions. Some integrations need special access, such as permission to:

• Post journal entries
• View invoices
• Edit customer records

If these permissions are missing or outdated, the two systems cannot sync with each other. But how? The integration tries to push data, but the accounting tool blocks it because the user does not have the required rights. Now, this leads to several accounting problems, such as:

• Failed sync attempts
• Partial uploads
• Missing transactions

The issue often comes up when roles change, new users are added, or software updates reset permission settings.

5. Manual Mistakes + Duplicate Records Confuse the System

When you enter data manually, even minor mistakes (like spelling a name differently or adding an extra space) create records that look similar but are not exact matches. Now, the system cannot decide which one is correct, so the sync fails or creates duplicates. 

Additionally, duplicates are sometimes created when you import data from multiple sources without checking if the customer or product already exists. During sync, the software does not know which record to use, which leads to several accounting problems, such as:

• Mismatched balances
• Missing invoices
• Repeated entries

So, the more manual touchpoints you have, the higher the chance of these sync conflicts.

6. Older Systems Cannot Handle Modern Integrations

Some D2C companies and consumer brands still use old accounting software that was built long before today’s integrations became common. These older systems may not support modern APIs, which are the “connectors” that let two tools share data. 

Without strong APIs, the software:

• Cannot accept data from other platforms

or

• May only support limited sync functions

This causes delays, partial transfers, or complete failures when you try to connect new tools.

How Sync Problems Impact Your Day-to-Day Business Work?

When your accounting software fails to sync with other systems, the impact goes beyond a small technical issue. It leads to several accounting problems, such as:

• Creation of gaps in your financial data
• Slowing down of routine tasks
• Forcing your team to spend time fixing errors instead of focusing on real work. 

For more clarity, let’s see how these issues affect your operations:

How to Prevent Accounting Sync Problems?

Do you know about the average annual cost of poor data quality? According to Gartner, it is estimated at $15 million per enterprise. And the main reason for such unreliable data? It is due to “sync failures”. 

To avoid sync-related accounting problems, your team can follow these best practices:

1. Review And Update Your Field Mappings Regularly

Each software uses its own fields for:

• Customers
• Products
• Taxes
• Payments

Mapping tells one system where to place data in the other. If these mappings are outdated or incorrect, the sync will fail or send data to the wrong place. Thus, your staff must review them regularly to make sure both systems remain aligned. Such a review should be particularly made after the introduction of new features or changes in your accounting setup.

2. Give Users The Right Permissions

Integrations only work when the connected user account has full access to the areas needed for the sync. Missing permissions (like access to journal entries, invoices, or customer records) cause blocked or partial data transfers. 

Thus, your internal teams should review user roles and make sure the integration user has complete access to all required modules.

3. Refresh Imports and Check Sync Status After System Changes

When you make changes inside your accounting system (like adding new accounts, updating tax rules, or editing product information), the integration may not recognize these new items. 

But why? That’s because the other connected system is still using the old structure, so both platforms stop matching. Now, because of this mismatch, there could be several accounting problems:

• The sync may fail
• Skipped entries
• Sending data to the wrong place

Okay, so what’s the solution? Your team should try to refresh or update the integration settings. They should try to refresh data imports + check the “sync status”. These assessments allow the integration to read the latest structure, which prevents mismatches and missing entries.

4. Use Tools That Provide Error Logs and Alerts

An integration tool with error logs shows you exactly where the sync failed. It points out:

• Missing fields
• Permission problems
• Mismatched records

This saves time during troubleshooting and reduces manual checking across systems.

5. Keep Your Internet Stable + Your Software Updated

A broken connection or outdated software can interrupt or block the sync. In contrast, a stable internet line allows continuous data transfer. Thus, to avoid accounting problems, your team should regularly update the accounting tools with:

• New features
• Security patches
• Fixes for known bugs

Can’t Resolve Your Sync Problems? Why Remain Stuck When You Can Outsource To Atidiv!

So now you know why several sync-related accounting problems get created. Let’s recap the primary reasons:

• Systems store and structure data differently, so information does not always match.
• Incorrect field mapping sends data to the wrong place or blocks the sync entirely.
• Missing user permissions prevent the integration from posting or updating records.
• Manual errors and duplicates confuse the system.
• Older platforms cannot support modern integrations.
• Internet drops and software glitches interrupt the transfer.

For many D2C companies and consumer brands, resolving these problems becomes costly and repetitive. If you are also unable to resolve your sync issues or are facing them repeatedly, you may hire a US accounting firm like Atidiv. 

We have 16 years of experience and 70+ global clients. Recently, we partnered with a NYC-based startup and helped it achieve 80% time savings and 50% cost savings.

Our expert team of 390,000+ chartered accountants and CPAs offers comprehensive bookkeeping services, strategic financial advisory, finance process design, and more. 

Get started at only $15 per hour. Let’s talk!

Accounting Problems FAQs

1. Why do duplicate invoices and payments keep happening in my accounting system?

The core problem is “mismatched records” across platforms. This leads to repeated invoices or payments slipping into your books. Additionally, duplicate entries may also occur because:

• Different systems send overlapping data
• Manual entries conflict with imports
• Sync processes fail midway

Studies show that usually businesses face a 1.2 to 1.29% duplicate rate.

2. How do disconnected systems increase sync failures?

When your CRM, ERP, POS, and accounting software are not connected through strong integrations, each system works alone. This creates “data silos,” which causes your sync to fail. 

The result? Your reports become unreliable, and staff spend time fixing mismatches instead of managing operations.

3. Which industries report the highest accounting sync failure rates in 2025?

In 2025, studies show that manufacturing faces the highest sync failure rate of 73%. That’s largely because their ERP systems are complex and hard to connect. 

After manufacturing, the e-commerce sector struggles due to multi-channel sales from Amazon, Shopify, Walmart, and others. Each platform sends data in a different format, making reconciliation and inventory matching more difficult.

4. How do sync-related accounting problems impact a small or midsize D2C company?

Usually, sync failures cause:

• Delayed invoicing
• Wrong balances
• Incorrect reports
• Extra manual work

Over time, these problems result in lost revenue, slow collections, and compliance risks. At an enterprise level, poor data quality can cost millions per year.

5. How can I prevent recurring sync-related accounting problems?

As a VP or director of a D2C company, you may start by:

• Reviewing field mappings
• Clearing duplicates
• Updating permissions
• Refreshing system settings after any change

Also, use integrations that provide “error logs” so you can pinpoint the exact failure.