Pros and Cons of QuickBooks (+ When to Upgrade)

QuickBooks is the default for ecommerce accounting, but as your business grows, its limits can cost you time, money, and peace of mind. What starts as a simple solution often becomes a daily headache as you add channels and orders. 

This guide breaks down the real pros and cons of QuickBooks for ecommerce, shows where it excels, and helps you decide when it is time to automate or move on.

When QuickBooks is the right choice for ecommerce

For many smaller ecommerce businesses, QuickBooks is all you need. The platform excels when your operation is simple: one sales channel, under 100 orders per month, and straightforward inventory. 

In these scenarios, QuickBooks delivers reliable value without unnecessary complexity.

QuickBooks is ideal for:

• Single-channel sellers (Shopify, Amazon, or your own website)
• Fewer than 100 orders per month
• Simple inventory (under 50 SKUs)
• Annual revenue below $250,000
• Teams needing basic expense and income tracking

Why it works:

• Low monthly cost
• Most accountants are already familiar with the platform
• Straightforward tax compliance and payroll add-ons
• Basic sales and expense reporting
• Quick setup and easy onboarding

Example scenario: A business selling handmade candles through a single Shopify store processes 40 orders monthly and tracks 12 SKUs. QuickBooks manages orders, reconciles payments, and supports timely tax filing. The owner spends less than five hours a week on accounting, and the monthly software cost stays under $50.

Table 1: When QuickBooks works and when it doesn’t

But as your business grows, new challenges emerge. Let us see how QuickBooks holds up as you scale.

Suggested read: QuickBooks Online vs. Desktop: Which Fits Your Business?

How QuickBooks performs at each growth stage

The pros and cons of QuickBooks shift as you move from startup to scaling. The right fit depends on your revenue, order volume, and channel complexity.

Table 2: QuickBooks for different growth stages

Self-assessment checklist:

• Which revenue range describes your business?
• How many sales channels do you manage?
• How many hours does your team spend on manual accounting tasks?
• When did you last oversell due to inventory mismatches?

At the scaling stage, manual QuickBooks processes often become a bottleneck. Many sellers add accounting automation platforms to handle the new complexity.

As your business grows, the real cost of managing complexity with QuickBooks starts to add up.

The true cost of QuickBooks: Beyond the monthly fee

The real cost of QuickBooks for ecommerce is often much higher than the monthly fee. Manual work, add-ons, and errors can double or triple your total spend.

Where the costs add up:

• Manual reconciliation: 10-15 hours per week at $30/hour = $1,200-$1,800 per month
• Add-ons: Inventory, payroll, and integration tools can add $500-$200 per month
• Error costs: Overselling, missed tax filings, and stockouts can cost thousands annually

So, what exactly can QuickBooks handle well and where does it start to break down?

Suggested read: QuickBooks Setup Preparation Guide for Ecommerce

QuickBooks features that break first for ecommerce

QuickBooks handles core accounting, but ecommerce complexity exposes key feature gaps.

Common pain points:

• Order-level detail and fee tracking: QuickBooks imports summary data, not individual order fees or marketplace deductions. This makes it hard to reconcile payouts and track true profitability by SKU or channel
• Refunds and returns: Refunds are not automatically matched to original orders, and inventory is not always updated in real time. Manual tracking increases error risk
• Inventory management: Basic inventory tools do not support real-time sync, multi-location tracking, or forecasting. Assembly, kit, and batch tracking require workarounds
• Multi-user and multi-channel: Permission controls are limited, and syncing across multiple channels is not native. Manual categorization is required for new channels or payment processors
• Reporting: Standard reports do not show SKU or channel profitability, customer acquisition cost, or returns by product. Exporting to spreadsheets is often required

Inventory is where most ecommerce sellers feel the pain first. Let us dig deeper.

Suggested read: How to Choose QuickBooks Inventory Management Software

Why inventory sync is QuickBooks’ fatal flaw for multichannel sellers

Inventory is the single biggest QuickBooks pain point for ecommerce at scale. QuickBooks cannot sync inventory across channels in real time, leading to overselling, stockouts, and hours of manual work.

What happens in practice:

• No real-time inventory sync between Shopify, Amazon, eBay, and POS systems
• Manual workarounds (spreadsheets, nightly updates) are error-prone and do not scale
• No forecasting, serial/lot tracking, or multi-location support at scale
• Overselling and stockouts result in lost sales and negative reviews

Scenario: You sell the same SKU on Amazon and Shopify. A customer buys on Shopify, but inventory on Amazon does not update instantly. Another customer buys on Amazon, and now you have oversold. You must process a refund, update inventory manually, and risk a negative customer experience.

Webgility connects all your sales channels, updates inventory instantly, and posts every order to QuickBooks automatically. Businesses like Epic Mens have saved hundreds of hours and scaled without adding staff.

If these inventory headaches sound familiar, you may have outgrown QuickBooks. Here is how to tell.

Suggested read: Best Free QuickBooks Connectors for Ecommerce

Signs you have outgrown QuickBooks (and what to do next)

Certain signs mean it is time to move beyond the pros and cons of QuickBooks alone.

Checklist:

• 3 or more sales channels
• 10+ hours per week on manual reconciliation
• Frequent overselling or stockouts
• No SKU or channel profitability reporting
• Multiple users needing access
• POS and online inventory never match
• Missed or late tax filings
• Needing to hire for manual entry
• Relying on spreadsheets for inventory
• Frustration with slow close or reporting

Scoring prompt: If you check five or more, you have outgrown QuickBooks.

ROI math: The cost of staying manual (lost time, errors, missed sales) often exceeds the investment in automation. For example, automating with Webgility can save up to 90% of reconciliation time and eliminate overselling..

Transition planning:

• Identify your top manual pain points
• Research automation or integration platforms that support your channels and QuickBooks
• Plan a phased transition to minimize disruption

If you are ready to automate, here is what to look for in a platform.

Suggested read: Should You Post Every Ecommerce Transaction to QuickBooks?

7 must-have features for QuickBooks automation platforms

Not all QuickBooks ecommerce automation platforms are equal. Here are the features that matter.

1. Real-time order and inventory sync
2. SKU-level profitability and reporting
3. Returns and refund automation
4. Robust support and onboarding
5. Multi-channel and POS commerce integrations
6. Platform ownership (your data, your QuickBooks file)
7. Flexible automation rules and scheduling

Webgility provides real-time sync, deep QuickBooks integration, and support for all major ecommerce and POS channels, trusted by over 5,000 businesses. Choosing the right platform ensures your accounting keeps pace with your growth.

Understanding the pros and cons of QuickBooks helps you evaluate whether native features or automation tools better serve your needs. 

QuickBooks excels at core accounting but struggles with multi-channel ecommerce complexity: manual order entry, limited marketplace fee mapping, and no real-time inventory sync.

Webgility solves these gaps by connecting QuickBooks to Shopify, Amazon, eBay, marketplaces, and POS systems with automated posting, fee reconciliation, and SKU-level profitability tracking.

Rider Shack, a surf and skate gear retailer managing over 13,000 products across Magento and QuickBooks POS, reduced operational costs and cancellations by $1,400 per month after implementing Webgility.

They saved 10-15 man-hours per week and reduced shipping processing time by 25% through automated inventory sync and proactive support that resolved issues in under 48 hours.

Book a demo with Webgility today.

Frequently asked questions (FAQs)

What are the biggest accounting headaches for ecommerce sellers using QuickBooks?

Many sellers struggle with manual reconciliation, inventory mismatches, and tracking profitability by SKU or channel. These issues grow as you add more sales channels and order volume.

How can I tell if I have outgrown QuickBooks for my ecommerce business?

If you spend over 10 hours weekly on manual tasks, manage multiple channels, or frequently oversell, it is time to consider automation or a new solution.

What is the main benefit of automating QuickBooks for ecommerce?

Automation saves time, reduces errors, and keeps inventory and orders in sync across all channels, helping you scale without hiring more staff.

Do I need to switch from QuickBooks if I add a second sales channel?

Not always. For low volume, QuickBooks can work, but adding automation tools is recommended to avoid manual errors and inventory headaches.