Managing a Shopify store is one thing, but juggling orders, inventory, and accounting? That’s a whole different beast. QuickBooks makes keeping track of finances a lot easier, but without the right integration, syncing sales and expenses can feel like herding cats. Luckily, there are apps designed to bridge the gap, automating the flow between Shopify and QuickBooks so you can spend less time on spreadsheets and more time growing your business. In this guide, we’ll break down the best options out there, what makes each stand out, and how to pick the one that actually fits your workflow.
Extuitive: Simplifying Shopify Ad Creation and Testing
Our platform Extuitive helps Shopify store owners turn ideas into high-performing ads quickly and efficiently. By connecting your store, our platform uses AI to generate ad concepts, test them against thousands of simulated consumer profiles, and predict which campaigns are most likely to succeed before any budget is spent. This makes ad creation faster, more accurate, and easier to manage.
Extuitive also streamlines campaign validation and optimization. From generating copy and visuals to analyzing performance metrics like impressions, clicks, and engagement, our platform provides actionable insights that help merchants see what works and make data-driven decisions. By combining predictive testing with real-time feedback, Extuitive enables Shopify stores to improve ad performance, save time, and grow their business with confidence.
Best Apps to Seamlessly Connect Shopify with QuickBooks
1. Zapier
Zapier offers a platform that connects Shopify and QuickBooks Online to automate the flow of data between the two systems. They allow users to create workflows, called Zaps, that trigger actions in one app based on events in the other. For example, when a new order is paid in Shopify, Zapier can automatically create a sales receipt in QuickBooks Online. This reduces the need for manual data entry and helps maintain consistent records across both platforms. Users can also update inventory or generate invoices automatically, keeping information synchronized without constant oversight.
The platform is designed to be flexible and approachable, with a visual workflow builder that doesn’t require coding experience. They provide templates for common use cases, making it easier to start automating tasks quickly. Overall, Zapier focuses on connecting apps in a way that simplifies repetitive processes and ensures that Shopify and QuickBooks Online data stays aligned.
Key Highlights:
- No-code automation between Shopify and QuickBooks Online
- Pre-built workflow templates for common actions
- Updates inventory, generates invoices, and syncs customer data
- Visual workflow builder for easy setup
- Integrates with thousands of other apps for extended automation
Who it’s best for:
- Small business owners who want to reduce manual bookkeeping
- Teams managing inventory across multiple platforms
- Anyone needing automated invoice generation
- Users looking for flexible, no-code workflow automation
Contact Information:
- Website: zapier.com
- Shopify App Store: apps.shopify.com/zapier
- Facebook: www.facebook.com/ZapierApp
- Twitter: x.com/zapier
2. Synder
Synder provides a platform that connects Shopify with QuickBooks to automate accounting tasks and reduce manual data entry. They allow users to sync sales, fees, taxes, and refunds from multiple sales channels directly into QuickBooks. The system also supports custom transaction mapping and metadata management, giving teams the ability to adapt the workflow to how they handle accounting internally. By automating categorization and reconciliation, Synder helps maintain consistent financial records without needing constant manual oversight.
The platform is built to handle high-volume and complex accounting environments, including subscription revenue recognition and audit-ready reporting. Users can connect multiple sales channels and configure the system to reflect their specific accounting practices. This makes it easier for teams to track financial data across Shopify and QuickBooks while maintaining compliance and accuracy.
Key Highlights:
- Automatic sync of sales, fees, taxes, and refunds
- Customizable transaction mapping and metadata handling
- Revenue recognition for subscription-based sales
- Supports multiple sales channels and accounting systems
- End-to-end encryption with SOC 2 Type 2 and GDPR compliance
Who it’s best for:
- Ecommerce retailers managing high sales volume
- Teams handling subscription-based revenue
- Accounting professionals needing detailed transaction tracking
- Businesses that want automated reconciliation and reporting
Contact Information:
- Website: synder.com
- E-mail: help@synder.com
- Shopify App Store: apps.shopify.com/synder
- Facebook: www.facebook.com/SynderHQ
- Twitter: x.com/SynderApp
- LinkedIn: www.linkedin.com/company/synder
- Instagram: www.instagram.com/synderapp
- Address: 1390 Market Street, Suite 200 San Francisco, CA 94102
- Phone: (415) 539-2507
3. A2X
A2X provides a system for connecting Shopify with QuickBooks that focuses on reconciling sales, fees, and taxes into organized summaries. They take raw payout data from Shopify and transform it into structured entries that match deposits in QuickBooks, helping teams maintain accurate books. The platform also allows users to assign rules to different types of transactions, which simplifies tracking taxable and non-taxable sales across regions. By automating the organization of financial data, A2X reduces the manual effort needed to keep accounting records aligned with actual store activity.
In addition to syncing transactions, A2X offers reporting tools that give visibility into profit margins, costs, and channel performance. Teams can monitor detailed financial statements without needing to spend hours processing raw data. The platform is designed to support multiple sales channels and integrates with several accounting systems, giving users flexibility in managing their ecommerce operations and bookkeeping practices.
Key Highlights:
- Automatically reconciles Shopify sales, fees, and taxes in QuickBooks
- Supports rules for transaction categorization by type and region
- Provides detailed financial reporting for profit and cost tracking
- Integrates with multiple accounting systems and sales channels
- Reduces manual bookkeeping effort and errors
Who it’s best for:
- Ecommerce businesses with multiple sales channels
- Teams needing accurate and detailed financial statements
- Accounting professionals handling frequent Shopify transactions
- Businesses aiming to streamline reconciliation and reporting
Contact Information:
- Website: www.a2xaccounting.com
- E-mail: contact@a2xaccounting.com
- Shopify App Store: apps.shopify.com/a2x
- Facebook: www.facebook.com/a2xaccounting
- Twitter: x.com/a2xaccounting
- LinkedIn: www.linkedin.com/company/a2x-for-ecommerce
4. MyWorks
MyWorks offers a platform that connects Shopify with QuickBooks to simplify accounting workflows. They focus on syncing customers, sales, inventory, and pricing between platforms, allowing financial data to stay aligned without constant manual updates. The platform supports both QuickBooks Online and Desktop, giving teams flexibility in how they handle ecommerce accounting. With frequent syncing options, users can ensure that records are consistently up to date, which helps maintain accurate books across their store and accounting system.
Beyond basic syncing, MyWorks provides tools for managing historical data and mapping custom fields between Shopify and QuickBooks. Their support network and resources aim to help teams troubleshoot and optimize integrations, making setup and ongoing management more manageable. The platform is designed to scale with growing businesses, allowing higher order volumes to be processed automatically without adding extra manual effort.
Key Highlights:
- Syncs customers, sales, inventory, and pricing between Shopify and QuickBooks
- Supports both QuickBooks Online and Desktop
- Allows custom field mapping and historical data sync
- Offers flexible sync intervals from minutes to hourly
- Provides 24/7 support and detailed learning resources
Who it’s best for:
- Ecommerce businesses handling frequent Shopify transactions
- Teams that require both online and desktop QuickBooks compatibility
- Stores needing flexible syncing options for orders and inventory
- Accounting teams looking for accessible support and resources
Contact Information:
- Website: myworks.software
- E-mail: hello@myworks.software
- Shopify App Store: apps.shopify.com/partners/myworks-software
- Facebook: www.facebook.com/myworkssoftware
- Twitter: x.com/myworkssoftware
- LinkedIn: www.linkedin.com/company/myworks-software
- Instagram: www.instagram.com/myworkssoftware
- Phone: (972) 505-3245
5. QuickBooks Connector (OneSaas)
QuickBooks Connector, formerly known as OneSaas, offers a tool to connect Shopify with QuickBooks Online for syncing financial and sales data. They focus on providing flexible synchronization options, letting users choose automatic or manual syncs depending on their workflow. The platform allows setting an integrations start date and timezone, giving teams control over how and when their data is pulled and updated. It also handles data cleanup and anonymization in line with privacy regulations, ensuring that old or sensitive data doesn’t interfere with ongoing accounting processes.
The connector supports syncing a range of financial records, including invoices, payments, and sales transactions, keeping Shopify and QuickBooks aligned. Users can manage their settings from a central dashboard, making it easier to monitor integration status and trigger immediate updates when necessary. This approach allows businesses to maintain consistent bookkeeping without needing constant manual intervention, making financial reconciliation smoother.
Key Highlights:
- Supports both automatic and manual synchronization
- Allows selection of integration start date and account timezone
- Handles invoices, payments, and sales data
- Performs data cleanup and anonymization for privacy compliance
- Centralized dashboard for managing sync settings
Who it’s best for:
- Businesses that need flexible control over when data syncs
- Teams handling multiple Shopify orders with QuickBooks Online
- Accounting staff looking for centralized integration management
- Stores that require compliance with global data privacy standards
Contact Information:
- Website: quickbooks.intuit.com
- Shopify App Store: apps.shopify.com/qbconnector
- Facebook: www.facebook.com/IntuitQuickBooks
- Twitter: x.com/QuickBooks
- LinkedIn: www.linkedin.com/showcase/quickbooks
- Phone: 1.800.264.1981
6. Amaka
Amaka provides tools to connect Shopify with QuickBooks Online, focusing on automating the flow of sales, payments, inventory, and cost of goods sold into accounting systems. They offer integration options that are straightforward to set up and manage, letting users synchronize data in near real-time or on a schedule that fits their workflow. In addition to standard integration features, Amaka also offers managed reconciliation services, where their team can review and reconcile accounts for businesses that want additional oversight.
The platform supports a variety of ecommerce and POS channels, including Shopify, Square, WooCommerce, and more, allowing multiple sales sources to feed into QuickBooks accurately. Users can also back-sync historical transactions for up to a year depending on the plan, which helps bring older data into alignment. With centralized dashboards and monitoring tools, businesses can keep track of synced transactions and ensure that books remain consistent without manually handling each order.
Key Highlights:
- Syncs sales, payments, inventory, and COGS to QuickBooks Online
- Supports multiple ecommerce and POS channels
- Offers managed reconciliation services
- Centralized dashboard for monitoring integrations
- Back-sync historical transactions for up to a year
Who it’s best for:
- Businesses with multiple sales channels needing consolidated accounting
- Teams looking to reduce manual bookkeeping
- Stores that want optional managed reconciliation support
- Companies that require flexible syncing schedules
Contact Information:
- Website: amaka.com
- Shopify App Store: apps.shopify.com/partners/amaka1
- Facebook: www.facebook.com/amakaApp
- Twitter: x.com/IoAmaka
- LinkedIn: www.linkedin.com/company/amakaintegrations
7. Webgility
Webgility helps ecommerce businesses connect Shopify with QuickBooks by automating the flow of orders, fees, refunds, and payouts into accounting systems. Their platform is designed to work in real time, updating books as sales happen and reducing the need for spreadsheets or manual entry. It also tracks inventory and cost of goods sold, giving a clearer picture of profit margins and helping businesses reconcile accounts more efficiently.
The tool supports multiple sales channels and integrates with various POS systems, which is useful for businesses selling on Shopify alongside other marketplaces. Users can get real-time reporting and AI-powered syncing that flags potential errors and adapts to different setups, making it easier for accounting teams to manage high volumes of transactions. The system aims to simplify bookkeeping while keeping records organized and audit-ready.
Key Highlights:
- Real-time syncing of orders, payments, refunds, and fees
- Tracks inventory and cost of goods sold (COGS)
- Supports multiple sales channels and POS systems
- AI-powered error detection and smart mapping
- Produces audit-ready books with detailed reporting
Who it’s best for:
- Ecommerce businesses selling on multiple platforms
- Accounting teams handling high transaction volumes
- Shops that need real-time visibility into finances
- Businesses wanting to automate order and inventory reconciliation
Contact Information:
- Website: www.webgility.com
- E-mail: sales@webgility.com
- Shopify App Store: apps.shopify.com/partners/webgility-inc
- Facebook: www.facebook.com/webgility
- Twitter: x.com/Webgility_HQ
- LinkedIn: www.linkedin.com/company/webgility-inc-
- Instagram: www.instagram.com/webgilityinc
- Address: 1111 6th Ave STE 550 San Diego, CA 92121
- Phone: (480) 900-0904
8. Bold Commerce QuickBooks Sync
Bold Commerce QuickBooks Sync helps Shopify merchants move order, product, and customer data into QuickBooks Online with minimal manual work. The tool focuses on syncing sales and tax information while keeping product and customer records consistent between platforms. It also allows importing products and inventory from QuickBooks back into Shopify, giving merchants a two-way flow that can help reduce discrepancies.
Users can manage mappings for products, orders, and customers to ensure the data lines up correctly in QuickBooks. The app also handles tax settings and supports exporting historical orders, which makes reconciling books more straightforward. While it doesn’t remove the need for review entirely, the tool provides structured workflows that simplify bookkeeping for stores with regular sales activity.
Key Highlights:
- Two-way syncing between Shopify and QuickBooks Online
- Manage product, order, and customer mappings
- Export taxes and historical orders
- Import products and inventory from QuickBooks to Shopify
- Configurable settings to reduce duplicate entries
Who it’s best for:
- Shopify merchants who regularly process orders in QuickBooks
- Stores needing consistent product and customer records across platforms
- Businesses that want to simplify tax tracking and reporting
- Teams looking to reduce manual data entry in bookkeeping
Contact Information:
- Website: boldcommerce.com
- Shopify App Store: apps.shopify.com/quickbooks-online
- Facebook: www.facebook.com/BoldCheckout
- Twitter: x.com/bold_commerce
- LinkedIn: www.linkedin.com/company/boldcommerce
- Instagram: www.instagram.com/bold_commerce
9. Stock Sync ‑ Qty Update by SKU
Stock Sync focuses on keeping Shopify inventory up to date by connecting with a variety of product feeds and data sources. It can handle feeds in formats like CSV, XML, XLS, JSON, and more, while also connecting via APIs, FTP, Dropbox, or email. This allows Shopify stores to automate stock updates across multiple suppliers or warehouses without needing to manually adjust quantities.
The app supports scheduled updates, so inventory can be refreshed hourly, daily, or monthly depending on the store’s needs. While it mainly handles stock levels, it also provides flexibility in mapping SKUs and product identifiers to ensure that updates are accurate. The automation reduces the chance of overselling and keeps Shopify inventories aligned with the source systems, including QuickBooks when used in combination with accounting integrations.
Key Highlights:
- Supports multiple feed formats including CSV, XML, XLS, JSON
- Connects through APIs, FTP, Dropbox, email, and cloud storage
- Scheduled inventory updates to match store requirements
- SKU mapping and product identifier management
- Compatible with accounting and ERP systems for automated sync
Who it’s best for:
- Shopify merchants managing multiple suppliers or warehouses
- Stores needing frequent inventory updates without manual input
- Teams using QuickBooks or other accounting software for stock tracking
- Businesses aiming to reduce overselling and stock discrepancies
Contact Information:
- Website: www.syncx.com
- Shopify App Store: apps.shopify.com/stock-sync
- Facebook: www.facebook.com/syncXdata
- Twitter: x.com/SyncX_data
- LinkedIn: www.linkedin.com/company/sync-x
- Address: 5-13-05, Block 5, VSQ @ PJ City Centre, Jln Utara, 46200 Petaling Jaya, Selangor
10. SyncTools
SyncTools is a handy app if you want your Shopify store and QuickBooks Online to play nicely together without you constantly babysitting your books. It moves sales, refunds, taxes, and inventory data over automatically, and you can choose whether you want it summarized in big chunks or broken down into individual transactions - whatever works best for your accounting style.
One neat thing is that it can handle multi-region setups, so income and expenses get sorted by country, state, sales channel, or even product. That means you can actually see where your money is coming from and make sense of payouts across different stores or regions. Basically, it gives you both the bird’s-eye view and the fine-grained detail, all without endless manual entry.
Key Highlights:
- Offers summarized or individual transaction sync options
- Automatic categorization by country, state, sales channel, and product
- Syncs sales, refunds, taxes, fees, and COGS to QuickBooks
- Supports reconciliation by matching payouts with deposits
- Handles multi-store and multi-region setups
Who it’s best for:
- Merchants managing multiple Shopify stores
- Businesses needing detailed or summarized transaction-level accounting
- Stores operating in multiple states or countries
- Teams looking to reduce manual bookkeeping tasks
- Shops tracking revenue by product category or sales channel
Contact Information:
- Website: synctools.ai
- Shopify App Store: apps.shopify.com/quickbooks-connector
- Facebook: www.facebook.com/synctools.io
- Twitter: x.com/Synctoolsio
- LinkedIn: www.linkedin.com/company/synctools-io
- Instagram: www.instagram.com/synctools
- Phone: +1 323 672 3738
Conclusion
Wrapping things up, connecting Shopify with QuickBooks doesn’t have to feel like a juggling act. The tools we’ve gone through show that whether a store is just starting out or handling multiple channels, there’s a way to keep sales, inventory, and financial records flowing without constantly double-checking spreadsheets. Each app approaches the process a bit differently - some focus on straightforward automation, others give more room for custom mapping and complex accounting workflows - but the goal is the same: making financial management less of a chore.
It’s worth remembering that no integration is completely hands-off. Even with automation, a quick check on reconciliations or syncing can save headaches down the line. Picking the right tool comes down to the way your store operates and how much control you want over data. In the end, these apps are less about replacing careful bookkeeping and more about giving you the space to focus on running your store, rather than wrestling with numbers all day.
