The Best Bookkeeping Software for Auto Repair Shops

Running an auto repair shop is a hands-on business, but managing the books is just as important. Between tracking parts inventory, managing payroll, invoicing customers, and keeping up with tax obligations, things can get overwhelming fast. After testing several solutions, I’ve found that the right bookkeeping software can streamline your financial tasks, allowing you to focus on keeping the business running smoothly.

Here’s a breakdown of the best bookkeeping software options tailored for auto repair shops.


Top 5 Bookkeeping Software for Auto Repair Shops

Software Best For Key Features Pricing
FreshBooks Best for invoicing & ease of use Custom invoicing, expense tracking, time tracking, mobile-friendly Starts at $17/month
QuickBooks Online Best all-rounder for small shops Invoicing, payroll, inventory tracking, integration with repair software Starts at $30/month
Shopmonkey Best for repair-specific needs Auto repair shop management, invoicing, parts tracking, integrations Starts at $129/month
Xero Best for scalability Cloud-based, inventory management, payroll, multi-currency Starts at $13/month
Wave Best free option Free invoicing, expense tracking, receipt scanning, payment processing Free

FreshBooks: Best for Invoicing and Ease of Use

FreshBooks is a perfect solution for auto repair shops that want an easy-to-use bookkeeping system, especially for managing invoices and tracking expenses. Whether you’re billing customers for parts and labor or tracking mechanic hours, FreshBooks helps you stay organized and get paid faster.

  • Why It’s a Top Pick: FreshBooks shines when it comes to invoicing and expense tracking. Its simple, user-friendly interface allows you to create customized invoices for customers, making it easy to bill for labor, parts, and services. You can also track expenses and manage your cash flow from anywhere, thanks to the cloud-based system and mobile app.
  • Custom Invoices: FreshBooks allows you to create professional, branded invoices that clearly separate labor and parts costs. You can also automate reminders for unpaid invoices and accept online payments through the platform.
  • Expense Tracking: Track expenses like parts purchases, shop supplies, and equipment easily. FreshBooks also integrates with your bank, allowing you to automatically import and categorize transactions.
  • Mobile App: The FreshBooks mobile app allows you to manage invoices, track billable hours, and even snap photos of receipts right from your phone—perfect if you’re often on the shop floor.
  • Time Tracking for Labor: If your mechanics charge by the hour, FreshBooks offers built-in time tracking that integrates seamlessly with invoices, making it easy to bill customers accurately.
  • Pricing: Starts at $17/month for the Lite plan, which includes invoicing, expense tracking, and time tracking. Higher tiers offer more advanced features like team collaboration and advanced reports.

QuickBooks Online: Best All-Rounder for Small Auto Shops

QuickBooks Online is the go-to choice for many small businesses, including auto repair shops. With robust features like payroll, inventory management, and easy integration with other software, QuickBooks Online helps you keep track of every part of your shop’s financials in one place.

  • Why It’s Perfect for Auto Shops: QuickBooks Online is versatile enough to handle the complexities of an auto repair shop. From tracking parts inventory and labor costs to managing payroll for your mechanics, QuickBooks has you covered.
  • Invoicing & Payment Processing: Create professional invoices with itemized labor and parts, and send them directly to customers. You can also accept payments online, making it easier to get paid quickly. Automated reminders for overdue invoices ensure you never forget to follow up.
  • Inventory Management: QuickBooks allows you to track your parts inventory so you’ll always know what’s in stock. You can set reorder points for key components like filters, tires, and other high-use parts, ensuring you never run out when customers need repairs.
  • Payroll Integration: If you have mechanics or administrative staff, QuickBooks’ payroll feature helps you manage employee wages, taxes, and benefits, all within the same platform.
  • Integration with Auto Repair Software: QuickBooks Online integrates with many popular auto repair shop management systems like Shopmonkey and Mitchell1, allowing you to connect your financials directly with your shop’s workflow.
  • Pricing: Starts at $30/month for the Simple Start plan, with higher tiers offering features like multi-user access, inventory tracking, and advanced reporting.

Shopmonkey: Best for Auto Repair-Specific Needs

Shopmonkey is designed specifically for auto repair shops, combining shop management and accounting features in one platform. It’s more than just bookkeeping—it’s a full shop management system that helps streamline operations, from customer appointments to parts ordering and invoicing.

  • Why It’s Ideal for Repair Shops: Shopmonkey is built with auto repair shops in mind. It handles everything from scheduling appointments to managing customer communication, parts inventory, invoicing, and even customer payments. This all-in-one approach makes it a great choice for busy shops.
  • Auto Repair Management: Shopmonkey helps you manage your entire shop, including work orders, parts inventory, and service history. You can easily track repair jobs, assign mechanics, and keep customers updated with status alerts.
  • Invoicing & Estimates: Create detailed invoices that separate parts and labor costs. You can also send repair estimates to customers before work begins and turn those estimates into invoices with a click.
  • Parts Tracking: Track your parts inventory in real time, ensuring you have what you need for each repair job. Shopmonkey also makes it easy to reorder parts when your stock is running low.
  • Payment Processing: Accept payments directly through Shopmonkey, and integrate with QuickBooks for seamless accounting and financial management.
  • Pricing: Starts at $129/month for the Basic plan, which includes job tracking, invoicing, and payment processing. Higher tiers offer advanced features like advanced reporting, customer management, and integrations.

Xero: Best for Scalability

Xero is another excellent cloud-based bookkeeping solution that offers robust accounting features and scalability for growing auto repair shops. If you plan to expand or want more advanced financial tracking, Xero provides excellent flexibility and detailed reports.

  • Why I Chose It: Xero is perfect if you’re looking for a scalable solution that can grow with your business. Its real-time tracking features, multi-currency support, and powerful inventory management tools make it ideal for shops that handle a large inventory of parts.
  • Inventory Management: Xero helps you track your parts inventory and manage cost of goods sold (COGS). You can easily see what parts you have in stock, how much you paid for them, and when it’s time to reorder.
  • Invoicing & Payment Processing: Xero offers easy-to-use invoicing features, allowing you to send professional, detailed invoices to your customers. You can also set up online payment options so customers can pay you faster.
  • Payroll & Employee Management: Xero includes a payroll feature that helps you manage employee salaries, taxes, and benefits. If your shop has several mechanics or front desk staff, this is a great tool to manage payroll efficiently.
  • Cloud-Based Access: Like FreshBooks, Xero is entirely cloud-based, meaning you can access your financials from anywhere using a browser. This is perfect for shop owners who need to stay on top of their business while on the go.
  • Pricing: Starts at $13/month for the Starter plan, which includes invoicing, inventory tracking, and basic reporting. Higher-tier plans offer more advanced features like multi-currency support and payroll.

Wave: Best Free Option

If you’re running a small auto repair shop or just starting out, Wave offers a free solution with all the basics you need. Wave includes invoicing, expense tracking, and even receipt scanning—all for no cost, making it ideal for budget-conscious shop owners.

  • Why I Recommend It: For small auto repair shops with simple bookkeeping needs, Wave is a fantastic choice. It’s completely free and offers enough features to manage your shop’s financials, including invoicing, expense tracking, and receipt management.
  • Invoicing: Wave makes it easy to create professional invoices with detailed line items for labor and parts. You can send invoices directly to customers via email and track when they’ve been paid.
  • Expense Tracking & Receipt Scanning: Wave allows you to track all your shop’s expenses, including parts purchases, tools, and supplies. You can even snap photos of receipts and upload them directly into your accounting system for easy tracking.
  • Free Payment Processing: Wave also includes payment processing, allowing customers to pay invoices online. It charges standard transaction fees for credit card payments, but the invoicing and tracking features are completely free.
  • Mobile App: Wave’s mobile app allows you to manage invoices, track expenses, and scan receipts on the go, making it easy to manage your shop’s financials wherever you are.
  • Pricing: Free for invoicing, expense tracking, and receipt scanning. Payment processing and payroll are optional paid add-ons.

Key Considerations When Choosing Bookkeeping Software for Auto Repair Shops

1. Invoicing & Payment Processing

  • Look for software that allows you to create detailed invoices that separate labor from parts. FreshBooks, QuickBooks, and Shopmonkey excel in this area.

2. Inventory Management

  • Auto repair shops often need to keep track of a large inventory of parts. QuickBooks, Shopmonkey, and Xero offer strong inventory tracking features.

3. Payroll

  • If you have mechanics or office staff, payroll management is crucial. QuickBooks and Xero offer integrated payroll features that make it easy to handle employee wages, taxes, and benefits.

4. Scalability

  • As your shop grows, you’ll need software that can scale with you. Xero and QuickBooks are perfect for shops that expect to expand and need more advanced features.

5. Cost

  • If you’re looking for a free solution, Wave is unbeatable. For more advanced needs, QuickBooks and Shopmonkey offer great value, but at a higher cost.

Final Thoughts

For most auto repair shops, FreshBooks offers the perfect combination of invoicing, expense tracking, and ease of use. If you’re looking for a full-featured solution that integrates with payroll and inventory management, QuickBooks Online is the best all-rounder. Shopmonkey is excellent for auto repair-specific needs, while Xero is ideal if you’re planning to grow your business. For budget-conscious shop owners, Wave provides a solid, free option.

Whichever solution you choose, setting up the right bookkeeping software will save you time, streamline your operations, and keep your auto repair shop’s finances running smoothly!

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