9 Best QuickBooks Desktop Integrations for Multichannel Sellers

Managing inventory, tracking sales, and handling finances shouldn’t feel like a full-time job. You’ve seen business owners talk about how QuickBooks Desktop integrations transformed their workflows. You’ve read the reviews, compared solutions, and even bookmarked a few options. 

But one thought keeps bothering you: Do they actually work? What if they cause errors in your financial data? What if they end up being more complicated than they’re worth?

In fact, you need to choose an integration solution that works with your version of QuickBooks Desktop without constant updates, compatibility issues, or a steep learning curve. The correct integration automates these tasks without forcing you to enter data manually.

In this guide, we’ll explore different QuickBooks Desktop integrations, including what they do, how they work, and which one might best fit your business. 

9 popular QuickBooks Desktop integrations for multichannel sellers

Here's a quick look at nine QuickBooks Desktop integrations that simplify everything from syncing your ecommerce platforms to processing payments, shipping, and managing customer relationships.

1. Ecommerce, POS, store integrations

For multichannel sellers, integrating your ecommerce platforms, POS systems, and stores with QuickBooks Desktop simplifies operations. Let’s explore three top integration platforms: Webgility, A2X, and Synder.

Webgility

Webgility connects your entire multichannel operation to QuickBooks Desktop, eliminating the need for tedious manual data entry and complicated reconciliations. It syncs orders, inventory, sales data, and payouts from platforms like Shopify, Amazon, Walmart, eBay, Etsy, Lightspeed, and more directly into your accounting system. The integration helps you manage everything in real time, so you never have to worry about mismatched numbers or inventory errors. 

From automating purchase orders and tracking fees to syncing product listings and pricing across all channels, Webgility simplifies your accounting tasks. With built-in business analytics, you can monitor sales trends and customer insights to make data-driven decisions.

Key features

• Expanding sales reach: Connect stores, marketplaces, and POS systems with QuickBooks Desktop using Webgility’s integration for Shopify, Amazon, Walmart, eBay, Etsy, Lightspeed, and more
• Automate order management: Post sales, returns, and fees to QuickBooks Desktop without manual entry
• Automate reconciliation: Record income, expenses, and payouts in the correct accounts for easier balancing
• Sync product listings: Sync product catalogs to create and update listings in your sales channels and QuickBooks
• Automate inventory and pricing: Update inventory levels and pricing across all sales channels, fully compatible with QuickBooks Enterprise Advanced Inventory
• Automate purchase orders: Generate POs for vendors in QuickBooks Desktop based on stock levels
• Simplify tax filing: Record sales tax collected by jurisdiction from all sales channels for compliance
• Capture marketplace fees: Sync fees from Amazon Settlement Reports, Shopify Payouts, and eBay Invoice Reports into QuickBooks
• Define order settings: Customize processing rules for B2C, B2B, or POS orders based on your needs
• Enable two-way pricing sync: Sync prices between sales channels and QuickBooks for consistency

Pricing

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

*all prices are billed annually

What are real-life users saying about Webgility?

“I really like the automatic sync of orders, inventory and funds with minimum effort at Webgility is connecting my Shopify store to QuickBooks. Their stand in all this is their own dashboard—it allows me to see all my sales and stock levels on any channel in a clear, real-time way without me having to pull my hair from manual updates.”

- Verified G2 review

A2X

As an accounting automation tool, A2X simplifies month-end reconciliation by capturing payout reports from platforms like Amazon and Shopify. It turns raw payout data into organized summaries that seamlessly reconcile with QuickBooks, Xero, Sage, or NetSuite.

However, A2X doesn’t provide real-time data syncing and is best suited for sellers using one or two platforms. It focuses only on summarized journal entries for revenue, sales tax, and fees, not individual transactions. It doesn’t integrate with other ecommerce, payments, or POS systems too.

As an A2X alternative, Webgility creates detailed accounting entries for each sale or summarized journal entries for revenue, sales tax, and fees.

Here’s a closer look at the other features Webgility offers over A2X:

Synder

Synder specializes in syncing ecommerce transactions and providing reconciliation tools. It integrates with QuickBooks, Xero, and Sage, making it a good option for businesses that need an accounting-first approach. 

If you're a small business looking for basic accounting automation, Synder might work for you, but it doesn't support larger, multi-channel operations like Webgility. While Synder is expanding its focus on SaaS, non-profits, and marketing agencies, ecommerce isn’t its main priority. Webgility, on the other hand, is built for ecommerce, with every new feature designed to meet your business needs.

2. Payment gateways

PayPal

For over 20 years, PayPal has led the way in digital payments, making financial services more convenient, affordable, and secure. With PayPal-QuickBooks Desktop integration, you can effortlessly connect your PayPal account to your ecommerce accounting software. 

This integration with Webgility tracks payments, fees, taxes, and more, automating the recording of PayPal fees, marketplace charges, expenses, and shipping costs for your online orders. Plus, if you’re selling on platforms like eBay or Shopify, Webgility ensures PayPal transactions across all channels are synced seamlessly to QuickBooks.

Key features

• Easy reconciliation: Match PayPal payouts with bank deposits automatically, so your accounts balance with ease
• Detailed reporting: Webgility provides a comprehensive breakdown of your PayPal transactions, including fees and taxes, so you can track expenses and revenues with clarity
• Multichannel support: If you’re selling on platforms like eBay or Shopify, Webgility ensures PayPal transactions across all channels are synced seamlessly to QuickBooks

Stripe

Stripe is a widely used payment gateway for businesses running subscription services or those that want a simple way to accept payments online. With the Stripe for QuickBooks integration, you can easily track Stripe transaction fees and automate the recording of all payment processor charges directly into QuickBooks.

You can also sync Amazon and other platform fees directly to your accounting software, making it easy to see exactly where your money is going. It also syncs marketplace fees, payment processor charges, and shipping costs, giving you a clear view of your cash flow. In addition, Webgility’s Stripe integration organizes sales tax data by jurisdiction, making sales tax filing less complicated and more accurate. 

Key features

• Real-time transaction syncing: Every payment, refund, and fee from Stripe is instantly updated in QuickBooks, ensuring that your accounting records are always current
• Customizable reports: Get detailed reports on Stripe fees, refunds, and taxes to simplify financial management and tax reporting
• Multiple channel support: Whether you’re using Shopify, WooCommerce, or another platform, Webgility ensures all Stripe transactions are adequately accounted for across all your sales channels
  
  

3. Shipping solutions

ShipStation

If you want a trusted shipping solution, ShipStation helps businesses process orders and shipments across multiple channels. The ShipStation-QuickBooks integration automatically syncs multichannel sales data and expenses into QuickBooks without using spreadsheets.

You can batch-post transactions to keep your books tidy or opt for more detailed data. Track fees, expenses, payment processor charges, and shipping costs, giving you a clear view of your finances and making expense management more effortless.

Key features

• Automate ShipStation accounting: Connect ShipStation and your online sales channels to post sales data to your accounting system automatically
• Performance insights: View your entire multichannel ecommerce performance from one dashboard to make smarter financial decisions
• Sales tax filing: Track and validate sales tax charges effortlessly, with all data neatly organized by jurisdiction in your accounting platform

ShipRush

With over 200 parcel and LTL carriers and 90+ ecommerce and accounting integrations, Descartes ShipRush simplifies multi-channel shipping for businesses. Through a quick QuickBooks integration, you can sync orders instantly and benefit from real-time rate shopping to find and pick the best shipping options easily. 

You can also choose to use your own negotiated rates or access discounts of up to 89% off retail prices from USPS, UPS, and FedEx.

ShipEasy automates tasks like presetting shipment weight, selecting specific shipping services, and more. You can customize email communications, tracking pages, shipping labels, and packing slips to create a standout brand experience.

Key features

• Recurring task automation: Set up rules to automate shipment details, like weight and service selection, saving you time
• Branded experience: Customize email communications, tracking pages, labels, and packing slips to enhance customer loyalty
• Shipping rate discounts: Save up to 89% on shipping with discounts from USPS, UPS, and FedEx
  
  

CRM and marketing tools 

HubSpot

If you're looking for a CRM solution to connect QuickBooks Desktop with HubSpot, SYNC for QuickBooks is another excellent option. Its automated synchronization keeps your financial records, customer details, orders, invoices, and payments current and accurate. 

The bi-directional sync keeps your records clean and up to date, whether the data originates in HubSpot or QuickBooks. Everything from customer details to purchase history stays connected, so your teams can automate workflows, trigger personalized follow-ups, and use synced data in reports without ever leaving HubSpot.

However, if you want to connect QuickBooks Desktop and HubSpot, you can do so with the SYNC for QuickBooks solution developed by Commercient. It integrates with over 150+ ERP systems, and you can directly connect data, such as customers, orders, invoices, inventory, and products, from QuickBooks Desktop into HubSpot. 

Key features

• Simplify billing and invoicing: Convert Quotes and Deals into invoices or subscriptions in just a few clicks, or create invoices from scratch. Push published invoices to QuickBooks automatically and sync payment updates from either system
• Track sync health easily: Track sync status in real time with detailed health reports, and quickly resolve errors using clear diagnostics and guidance
• Customize field mappings: Use Operations Hub Starter or above to tailor your invoice, contact, and product sync fields to ensure your data flows seamlessly between platforms without compromising structure

Mailchimp

Renowned as the #1 email marketing and automation platform, Intuit Mailchimp offers smart recommendations to boost opens, clicks, and sales while helping you win new customers. The platform makes content creation faster and easier with generative AI tools and lets you choose from expert templates tailored to your industry. 

You can also connect MailChimp with QuickBooks Online to use transaction data to send highly targeted campaigns based on what customers have bought, how much they've spent, or the last payment you received. 

Plus, seamless integrations with tools like Canva, Shopify, WooCommerce, QuickBooks Desktop, and more allow you to sync data from your ecommerce platforms and marketing tools. 

Key features

• 1-on-1 communication: Mailchimp Inbox allows sales or support teams to collaborate and respond quickly, ensuring personalized customer interactions and driving sales
• Email automation: Automated emails based on customer behavior can boost open rates by up to 93% and increase click-through rates by 174%
• Advanced tools for multichannel campaigns: Leverage segmentation tools, tags, and financial insights to craft targeted campaigns, with a 23% higher open rate and a 49% higher click-through rate

Getting started with QuickBooks Desktop integration

Setting up QuickBooks Desktop integrations requires careful planning and an understanding of your business’s needs. 

Here's a step-by-step guide to ensure a smooth setup process:

1. Choose the right integration based on your business model

If you sell on platforms like Shopify or Amazon, you need an integration that automatically pulls in order details, taxes, and shipping costs. If you operate on multiple ecommerce platforms, you’ll want an option that consolidates data instead of managing each platform separately, such as Webgility. 

If your business is service-based, look for an integration that tracks invoices, payments, and project expenses without extra effort. If you handle inventory, ensure your integration updates stock levels in real time so you don’t sell something you don’t have.

2. Verify compatibility with your QuickBooks Desktop version

QuickBooks Desktop comes in different versions, including Pro, Premier, and Enterprise, and not every integration works with all of them.

The right QuickBooks Desktop version matters as much as the integration you choose since each offers different features and limitations. Here’s how different QuickBooks Desktop versions fit various business needs.

Before choosing the right solution, verify that it supports your QuickBooks version. For example, tools like Synder primarily focus on QuickBooks Online, not Desktop. Similarly, Webgility A2X works with all QuickBook variants, making it a solid choice for ecommerce businesses and payment reconciliation. 

HubSpot also integrates with all versions of QuickBooks, making it better suited for companies that rely on CRM data for sales tracking. PayPal and Stripe sync across all versions, helping with payments and marketing campaigns. 

3. Set up API connections and automation rules

Once you’ve chosen the integration that suits your business and is compatible with your QuickBooks version, it’s time to link the systems. Most integrations use API keys, login credentials, or direct connections to sync data between QuickBooks and external platforms.

During setup, you’ll be asked to connect your accounts. Some integrations will ask permission to access specific QuickBooks data, such as invoices, payments, or inventory. Ensure that these permissions are correctly set up to avoid syncing issues later.

Next, establish clear automation rules. Decide whether you want sales orders to sync automatically or manually and whether QuickBooks should update inventory levels with each sale. 

Think about syncing customer details and other data points requiring real-time updates. Setting these rules correctly will reduce errors and save time, allowing data to flow smoothly without needing manual corrections.

4. Test data sync before full implementation

Once you’ve set up your rules, run tests to verify that data syncs as expected. Start small—import a few sales orders, sync some invoices, or update inventory levels.

Webgility automatically captures data and allows you to sync it across various platforms without coding or complex APIs. Once the test data is in QuickBooks, review the following to check for accuracy:

• Are transactions assigned to the proper accounts?
• Do the taxes and payment amounts match?
• Are customer records updating correctly?

If anything seems off, adjust the settings before fully automating. 

Next, you can sync inventory and prices and generate purchase orders for stock replenishment. You can also automate catalog listings for further efficiency. Predefined mappings and an easy-to-use wizard simplify setup, allowing Webgility to sync data smoothly across your systems.

Catching issues early helps you avoid messy financial records and time-consuming fixes later. Once the test run is successful, you can confidently scale up the integration.

Try Webgility for QuickBooks Desktop integration

A 2023 study revealed that 53% of ecommerce sellers spend between 1 and 10 hours a week just on inventory management. If you don’t have the right setup, this time-consuming task can lead to errors that impact your profits and productivity.

Webgility for QuickBooks Desktop connects with your online stores, keeping your pricing, sales data, and inventory accurate across all platforms. It automatically syncs your orders, payments, and financial details, so you don’t have to spend hours fixing numbers. 

Even if you sell across multiple platforms, Webgility tracks sales tax from all channels, making tax filing much easier.

Join the 5,000+ businesses already saving time, reducing costs, and boosting profits with Webgility. Get started today and see the difference it can make.

FAQs

How can I connect my ecommerce store to QuickBooks Desktop?

Webgility allows you to connect your ecommerce store to QuickBooks Desktop. It automates data syncing between your store and QuickBooks, handling sales, inventory, and financial data.

What tools automate bookkeeping for QuickBooks Desktop?

Tools like Webgility and Synder automate bookkeeping by syncing sales, inventory, and financial data into QuickBooks Desktop. 

How do I set up QuickBooks Desktop integrations for inventory management?

To set up QuickBooks Desktop integrations for inventory management, choose a compatible integration tool, sync your online stores, configure settings, and automatically automate inventory tracking, syncing sales and stock data. Webgility, for instance, updates stock levels, prices, and product details for smooth inventory management across systems.