Thrift Store Accounting Software: 7 Best Solutions

10:25

We get it: Thrift store finances are a headache.

You spend your nights crunching numbers, trying to reconcile last month’s donations with actual sales, and struggling to get the numbers to match up.

And because managing operating costs in a thrift store isn't like running a regular retail business, generic accounting software can sometimes hurt more than it helps.

Retail systems expect you to purchase inventory at fixed costs. Nonprofit platforms focus on fundraising campaigns but ignore your daily sales operations. When you’re running a nonprofit retail business, you end up using multiple tools that don't talk to each other, bookkeeping by manually entering the same data twice, and crossing your fingers during audit season.

It doesn’t have to be this way.

In this guide, we’ll explore seven accounting software solutions built for the messy reality of thrift store finances.

Why Thrift Stores Need Specialized Accounting Software

Before we get into our top solutions for thrift stores, let’s lay some groundwork. Thrift stores need unique tools to manage their unique finances. But in order to select a tool that helps you solve your challenges, you need a firm understanding of what those challenges are:

Zero-cost inventory tracking: Donations arrive without purchase prices, but you still need accurate values for insurance claims, grant applications, and financial reporting.
Unpredictable supply chains: Donations surge during the spring cleaning season and decline in winter, creating wild swings in inventory levels that make forecasting impossible.
Multiple revenue streams: Most thrift stores have revenue from retail sales, roundup donations at checkout, and grant funding.
Nonprofit compliance requirements: Form 990 preparation, donor acknowledgment letters, and unrelated business income tax (UBIT) considerations make your accounting processes more complex.
Volunteer hour tracking: You need detailed records of volunteer hours for the IRS and most grant applications.
Tax-exempt transactions: Processing tax-exempt sales requires detailed record-keeping.
Donor receipt generation: Manually creating tax receipts for donation dropoffs can be a time-consuming process.

With the right accounting software, you can save time, money, and stress. A thrift store accounting software solution has the features and functionality you need to manage all these challenges in one central tool.

Let’s take a look at the top options to consider.

1. QuickBooks Online (Nonprofit Edition)

QuickBooks Online is the number-one industry-standard accounting platform. Its nonprofit edition includes features specifically designed for charitable organizations like thrift stores. QuickBooks is popular with businesses across industries because it’s an all-in-one solution that handles day-to-day bookkeeping and complex thrift store accounting needs.

Key features:

Fund accounting and grant tracking
Donor management capabilities
Class and location tracking
Form 990 preparation support
Integration with point of sale (POS) systems

Pricing: Starting at $30/month (nonprofit discount available)

QuickBooks is a strong fit for established thrift stores or businesses with lots of tools that need a solution with flexible integrations — but you still need separate tools for donation tracking and inventory management.

2. Xero

Xero is a cloud-based accounting platform known for its easy-to-use interface. It's particularly popular with growing businesses because it starts at a small price point but can scale reasonably well as the company grows. The platform's unlimited user feature means your entire team can get into the platform without paying per-seat fees.

Key features:

Unlimited users on all plans
Real-time bank reconciliation
Multicurrency support
Simple inventory tracking

Pricing: Starting at $13/month

Xero is a strong fit for growing thrift stores with many employees who need accounting access. The challenges with this solution are that it has limited nonprofit-specific features. If you want the same nonprofit reporting features as a solution like QuickBooks, you have to purchase add-ons.

3. Aplos

Aplos is an accounting tool built specifically for nonprofits and churches. It combines fund accounting with donor management. The platform also has strong reporting features, which are a great fit for thrift stores that need advanced reports for grant applications.

Key features:

Fund accounting
Donor management and online giving tools
Automated donation receipts
Advanced financial dashboards

Pricing: Starting at $59/month

Aplos works well for nonprofit thrift stores that prioritize grant compliance, but it has limited inventory features and doesn’t offer as many integrations as QuickBooks or Xero — this means there’s a chance you’ll have siloed data between systems, depending on your existing tool stack.

4. Wave Accounting

Wave offers free accounting software designed for small businesses on shoestring budgets. It lacks some of the advanced features found in other solutions on this list — but for new thrift stores or tiny operations, it covers the fundamentals surprisingly well.

Key features:

Unlimited invoicing and expense tracking
Bank connection and reconciliation
Receipt scanning via mobile app
Basic financial reporting

Pricing: Free (payment processing fees applied if you use Wave Payments)

Wave is best for small, single-location thrift stores, but their “free” status comes with some challenges. First and foremost, their customer support is lacking (and only available through an online help portal). You also won’t have access to features like fund accounting or donor management tools.

5. Sage Intacct

Sage Intacct is an enterprise-level financial management system designed for larger nonprofits. It's the solution that major thrift store chains and organizations with dozens of locations switch to when QuickBooks no longer cuts it.

Key features:

Advanced fund accounting with sophisticated tracking
Multi-entity and multilocation management
Grant management and compliance tools
Powerful automation capabilities

Pricing: Custom pricing (typically starts around $400/month)

Sage Intacct usually works best for large chains like Goodwill or Salvation Army, but it’s often too pricey for smaller operations. It’s also a complicated tool that requires professional implementation support and dedicated staff to keep it running.

6. FreshBooks

FreshBooks is designed to be a simple solution for service businesses and freelancers. This simplicity might appeal to small thrift store operators who want basic tracking and don’t need advanced features. The solution offers strong time tracking features that work well for organizations that rely heavily on volunteers.

Key features:

Easy-to-use interface
Time tracking capabilities
Expense categorization
Mobile app

Pricing: Starting at $17/month

FreshBooks is a good option for small operations willing to prioritize simplicity over advanced features. The tool lacks nonprofit-specific features, like fund accounting and donor management. It also lacks inventory management features, meaning you’d need a separate tool to manage your inventory.

7. ThriftCart

ThriftCart is an all-in-one platform built specifically for thrift stores. Our system combines point of sale, donation tracking, inventory management, and financial reporting into a single system. It was created by thrift store operators who got tired of juggling five different systems just to run their stores and close their books each month.

Key features:

Donation intake tracking
Automatic tax receipt generation
Roundup donations at checkout
Advanced inventory management
Multilocation reporting
Sales and financial reports
E-commerce integration

Pricing: Custom pricing based on store size and needs

Our platform works best for thrift stores looking for an all-in-one solution that integrates with more advanced accounting software when needed. Unlike standalone accounting software, ThriftCart captures transaction data and organizes it for financial reporting. With our system, everything flows through one system, giving you cleaner data and faster month-end closes.

How To Choose the Right Thrift Store Accounting Software

Choosing accounting software starts with understanding your thrift store’s actual daily needs, not just picking the most popular (or cheapest) option. If you’re not sure where to start, use this simple checklist:

Nonprofit compliance needs: Do you need fund accounting for restricted grants, Form 990 preparation support, or donor management tools?
Integration requirements: Will the software connect with all the other tools you already use?
User-friendliness: Can your staff and volunteers learn it quickly?
Budget: What's the total cost, including setup fees, training time, and monthly subscriptions?
Support: Is help available when you actually need it?

All-in-one solutions handle all of these needs, while standalone accounting software might require you to prioritize a few of these features over others.

Streamline Your Thrift Store Accounting Software and Operations With ThriftCart

Thrift store accounting is complicated, but the right software makes it less of a headache. The seven tools discussed in this post all offer features you can use to make your finances run more smoothly. However, many only provide a few pieces of the overall financial puzzle, forcing you to invest in multiple tools or track some processes manually.

ThriftCart was built specifically for thrift stores and designed to give you everything you need to run your store in a single system — one platform, one login, complete visibility into your operations and finances.

Stop juggling disconnected systems. Build and price your ideal ThriftCart solution today to see how you can use our tools to simplify your thrift store accounting and operations.

Thrift Store Accounting Software: 7 Best Solutions