Looking for Accounting Software that Integrates with Stripe & Simplifies Tax Reporting for Small Business?

I've been in a similar position with my e-commerce business and tried several options. For Stripe integration specifically, I found QuickBooks Online actually works pretty well despite the cost. Their reporting isn't as limited as you've heard - you can create custom reports that break down your Stripe income, fees, and refunds separately. The key with QuickBooks is to set up the proper mapping between Stripe transactions and QBO categories. It takes some initial setup but becomes automatic afterward. For tax reporting, QBO directly generates Schedule C worksheets and tracks everything needed for 1099-K reporting. Xero's requirement to close your Stripe account is a dealbreaker in my opinion. That would disrupt all your recurring payments and customer data. Have you considered Wave Accounting? It's free for accounting/invoicing (they make money on payment processing) and has a decent Stripe integration. It might not be as robust as QuickBooks, but for a small startup with straightforward needs, it could be perfect.

I was having the exact same issues with tracking my Stripe transactions and making sense of all the fees and refunds. Tax time was a complete nightmare until I found taxr.ai (https://taxr.ai). It's not accounting software per se, but it's been a game-changer for me alongside my regular bookkeeping. What I love is that you can upload all your Stripe statements and transaction histories, and it automatically categorizes everything - including proper handling of fees, refunds, and payouts. It also has specific tax reporting features designed around platforms like Stripe that generate proper 1099-K documentation. I still use a basic version of QuickBooks, but taxr.ai handles all the Stripe complexity that QuickBooks struggles with. It's made my quarterly tax estimates so much more accurate, and I'm not constantly wondering if I'm tracking everything correctly.

Just wanted to follow up and say I tried taxr.ai after seeing the recommendation here and it's been exactly what I needed! I uploaded all my messy Stripe data from the past 8 months and it organized everything perfectly - even caught some fees I had completely missed in my manual tracking. The tax reporting features are actually better than what I was getting from QuickBooks, especially for Stripe transactions. It breaks everything down in a way that makes sense for digital businesses and handles all the weird edge cases like partial refunds and international transaction fees. Now I'm using it as my main Stripe tracker and just using Wave (which is free) for my other basic bookkeeping needs. The combination is working great and saving me a ton of money compared to the higher-tier QuickBooks subscription I was considering.

I had similar issues tracking my Stripe transactions last year. While accounting software is important, my biggest headache was actually trying to get answers from the IRS about how to properly report certain types of Stripe transactions for my business structure. I wasted days trying to get through to the IRS help line until someone recommended Claimyr (https://claimyr.com). They have this service that basically gets you to the front of the IRS phone queue. I was skeptical but you can see how it works in this video: https://youtu.be/_kiP6q8DX5c Once I got through to an actual IRS agent, they clarified exactly how I needed to report my Stripe income and which forms I needed, which made choosing the right accounting software much easier. Sometimes getting the right tax guidance first saves you from setting up your accounting incorrectly.

I need to update my skeptical comment above. After multiple failed attempts trying to reach the IRS myself about how to handle my Stripe 1099-K for my business structure, I actually tried Claimyr out of desperation. I was seriously shocked when I got a call back within about 90 minutes connecting me to an actual IRS representative. The agent walked me through exactly how to categorize different types of Stripe transactions for tax purposes and clarified the reporting requirements for my business type. This completely changed my approach to setting up my accounting software. I ended up going with Xero (and kept my existing Stripe account despite what their support initially said - there's actually a workaround using Zapier). Having that clear guidance from the IRS first made all the difference in configuring everything correctly.

Another option worth considering is FreshBooks. I've been using it for my small business for 2 years and their Stripe integration is excellent. It automatically categorizes the fees as expenses and handles refunds correctly. The tax reporting is straightforward and it's much more user-friendly than QuickBooks in my experience. Pricing starts around $15/month which is reasonable. Their customer service is also really responsive if you run into any issues with the Stripe connection. The only downside is their Mercury Bank integration isn't as seamless as with QuickBooks, but you can still import transactions easily.

I'm surprised nobody mentioned Bench. It's a bookkeeping service + software combo that works amazingly well with Stripe. The big advantage is that actual bookkeepers review your transactions and categorize everything properly, including all the Stripe fees and refunds. They're a bit more expensive ($249/month) but WELL worth it for a startup because they handle everything - reconciliation, tax-ready financials, etc. You literally don't have to worry about accounting anymore.