Best Link My Books Alternatives for ecommerce Accounting in 2025

If you run an ecommerce business, you’ve probably come across Link My Books, a reliable tool for syncing payouts from Amazon, Shopify, and eBay into QuickBooks Online or Xero. But as your operations scale, its simplicity can start to feel like a limitation rather than a strength.

A common complaint is the lack of inventory management and limited customization options, which makes it challenging for businesses with complex workflows or multiple sales channels. 

Users also note that scaling with Link My Books becomes expensive, without a corresponding increase in features or flexibility. Many growing ecommerce businesses are now seeking alternatives to Link My Books that offer broader integrations, deeper reporting, and greater scalability.

In this guide, we will break down the top five Link My Book alternatives, comparing their features, pros, cons, and pricing. 

Top 5 Link My Books alternatives: A quick comparison

Here’s a quick look at the top Link My Book alternatives:  

1. Webgility 

Webgility is an all-in-one ecommerce integration platform trusted by over 20,000 businesses to streamline their accounting, inventory, and order workflows. 

It is built specifically for businesses selling across multiple channels, connecting your ecommerce stores, marketplaces, and POS systems directly to accounting software like QuickBooks Online and QuickBooks Desktop.

Unlike tools with a more limited scope, Webgility goes beyond simple bookkeeping automation. It offers real-time order data sync, multichannel inventory management, financial analytics, and ecommerce reporting—all in one place. 

Additionally, it’s one of the few solutions powered by AI that makes reconciliation, forecasting, and reporting even smarter and faster.

Ideal for 

• Small businesses and large enterprises managing multiple online stores, marketplaces, and in-person locations
• Sellers who rely heavily on QuickBooks for their accounting
• Brands seeking a complete solution that covers inventory, order management, financial reporting, and automation

Why choose Webgility over Link My Books?

Key features 

• Real-time order sync across all channels: While Link My Books batches data based on settlement periods, Webgility syncs orders, returns, and refunds in real-time across Shopify, Amazon, eBay, Walmart, Etsy, and more
• Multi-channel inventory and order management: Link My Books mainly focuses on accounting, while Webgility offers centralized inventory and order management across all your sales channels. Thus, you can manage stock levels, pricing, and fulfillment rules in one place, avoiding overselling across marketplaces and your DTC store

“I found inventory control was my biggest challenge. Cross-posting on so many channels, it's easy to oversell. Webgility keeps my sales channels aligned perfectly.”

   - Kathleen Gallagher, CEO, Celtic Mink Jewelry

• Easy integration with POS systems:  Webgility isn’t just for online sales; it also integrates brick-and-mortar with major POS systems like Clover, Lightspeed, and Square, giving you complete visibility and synchronization between your online stores and physical locations
• Both summary and detailed accounting flexibility:  Webgility allows you to post either summaries or detailed individual transactions
• Advanced financial reporting and custom dashboards:  Webgility delivers robust analytics and fully customizable financial dashboards. Instead of relying solely on basic summaries, you can drill down into revenue, profitability, COGS, channel-specific expenses, from a single centralized dashboard

Pricing 

Webgility’s pricing suits businesses of all sizes: 

• Basic (Online): $49
• Pro (Online): $99/month
• Plus (Desktop): $109/month
• Advanced (Desktop): $199/month
• Premium (Desktop): $399/month

2. A2X

A2X transforms uncategorized ecommerce payout data into organized summaries that integrate easily with QuickBooks Online, Xero, Sage, or NetSuite. It’s a favorite among accountants and bookkeepers for speeding up month-end closings as it automatically captures payout reports and categorizes revenue, expenses, and sales tax.

Key features 

• Works with QuickBooks, Xero, Sage, and NetSuite
• Offers multi-currency support for international businesses
• Automatically organizes and summarizes payouts for easy, accurate bookkeeping and generates detailed financial reports to support month-end closing and tax filing

Pros 

• Accurate and reliable data synchronization that reduces manual errors
• Easy to set up and use
• Strong customer support with quick response times

Cons 

• Limited customization for workflows and mappings
• Not ideal for multi-channel sellers managing many platforms
• No built-in inventory management features
• Gets expensive with higher-order volumes

Pricing 

Starts at $29/month for up to 200 orders a month.

3. Synder

Synder is a smart accounting automation tool that connects multiple payment platforms, such as Shopify, Amazon, Stripe, and PayPal, with accounting software like QuickBooks, Xero, and QuickBooks Desktop. It simplifies bookkeeping by automatically syncing transactions, handling multi-currency operations, and generating detailed financial reports. 

Key features 

• Multi-platform integration with Shopify, Amazon, Stripe, PayPal, Square, and more
• Automatic synchronization of transactions into QuickBooks Online, Xero, and QuickBooks Desktop
• Real-time payment reconciliation and error detection

Pros 

• Easy-to-use interface, even for beginners
• Strong multi-currency and multi-channel capabilities
• Excellent customer support and onboarding help

Cons 

• Pricing can get expensive as order volume grows
• Limited inventory management 
• Occasional sync glitches with certain platforms 

Pricing 

The Basic plan starts at $52/month for up to 50 transactions.

4. Bookkeep 

Bookkeep simplifies financial workflows for ecommerce businesses, especially those handling multiple platforms. It automates daily sales summaries, payment reconciliations, and revenue posting into QuickBooks Online and Xero, helping businesses maintain clean, accurate books without manual entry.

Key features 

• Automated daily sales posting from platforms like Shopify, Amazon, Square, and Stripe
• Supports multi-location and multi-currency businesses

Pros 

• Very easy setup with minimal learning curve
• Reliable daily sales automation and revenue posting
• Strong customer support and quick response times

Cons 

• Limited integrations compared to competitors (only major platforms supported)
• No inventory management capabilities
• Reporting is basic; not ideal for businesses needing in-depth analytics
• Can get expensive as the number of connections and locations grows

Pricing 

The Starter plan starts at $49/month for basic sales automation.

5. Myworks Sync 

MyWorks Sync is a QuickBooks integration tool primarily built for WooCommerce users. It helps businesses automatically sync their orders, customers, products, and inventory between WooCommerce and QuickBooks (Online and Desktop), aiming to reduce manual data entry and streamline financial operations.

Key features 

• Two-way real-time sync between WooCommerce and QuickBooks (Online/Desktop)
• Supports multi-currency and multi-location QuickBooks setups
• Custom field mapping and flexible sync settings

Pros 

• Strong support for both QuickBooks Online and Desktop versions
• Helpful and responsive support team

Cons 

• Primarily suited only for WooCommerce users — no support for other ecommerce platforms
• Setup can be complex and time-consuming for beginners
• Expensive compared to broader multi-channel accounting solutions

Pricing 

The Starter plan starts at $19/month (up to 100 orders/month).

Features to consider when choosing a Link My Books alternative

1. Integration with multiple marketplaces and POS solutions

Integration with various marketplaces is a must-have for ecommerce businesses aiming to scale. As you grow, you’ll likely expand across different channels — and maybe even add physical stores.

Unlike Link My Books, which primarily focuses on a few platforms (such as Amazon, eBay, and Shopify), a solution like Webgility offers broader integrations, including Amazon, Walmart, Etsy, and major POS systems like Square, Clover, and Lightspeed, providing true multi-channel and omnichannel flexibility.

2. Advanced inventory and order management workflows

If scaling is on your roadmap, you’ll want a solution that supports multichannel order management based on rules for payment methods, channels, order status, and more. Webgility’s rules engine helps you streamline operations and eliminate manual work, allowing you to spend more time on strategy and growth.

3. Robust financial analytics and reporting

While Link My Books helps summarize payouts, it falls short on detailed reporting and real-time business insights.

Webgility, on the other hand, offers advanced financial analytics and customizable dashboards. You get a crystal-clear view of your ecommerce profitability, expenses, and performance across every sales channel, essential for data-driven decision-making.

Trust Webgility for deeper financial insights

If you're planning to grow beyond a few platforms or need deeper financial insights, Webgility is a stronger alternative to Link My Books.

Not only does Webgility offer a wider range of integrations and real-time data sync, but it also comes with award-winning onboarding and support teams that ensure you’re set up for success.

Get started for free with Webgility and experience how easy scaling your ecommerce accounting can be!

FAQs

What is the best Link My Books alternative?

Webgility is the best alternative as it offers real-time sync, full inventory and order management, advanced reporting, and support for multichannel ecommerce and POS systems.

What makes Webgility a better choice than Link My Books?

Unlike Link My Books, Webgility goes beyond basic accounting sync by offering real-time automation, detailed reporting, inventory management, POS integration, and AI-powered insights that are built to scale with growing ecommerce businesses.