Top Accounting Software Options (And How to Pick One Without Overthinking It)
Top Accounting Software Options (And How to Pick One Without Overthinking It)
If your accounting software feels confusing, outdated, or like it takes three clicks to do one simple thing, you’re not imagining it. A lot of shop owners limp along with a system that technically works, but does not fit the business they’re running now.
And when your bookkeeping system doesn’t fit, your numbers start feeling like a back room inventory bin that got knocked over. Everything is in there somewhere, but good luck finding what you need quickly.
In this post, I’m breaking down top accounting software options for small business owners, retail stores, and online sellers, plus what to look for so you can choose with confidence.
What the right accounting software should do for your shop
Before you compare brands, I want you to get clear on the job you need your accounting software to do.
Because the “best” accounting software isn’t universal. It depends on how you sell (in-store, online, or both), how many accounts you run, and how complicated your day-to-day money flow is.
Here’s what I want your system to handle without drama:
Sales clarity: You can see sales by channel (POS vs online) without guessing.
Fee tracking: Shopify, Stripe, Square, PayPal fees are recorded consistently.
Bank reconciliation: Your books match your bank, monthly, on purpose.
Clean reporting: Your Profit & Loss tells the truth, even when you’re busy.
Sales tax support: You can track what you collected and what you owe.
Scalability: It still works when your orders double or you hire help.
If this is the part you get stuck on, here’s a deeper dive that helps you see why messy systems get expensive fast: You Can’t Out-Earn Disorganized Finances
Also, if you’re trying to build stronger money habits (without making it a full-time hobby), you’ll probably like the downloads in my resource library.
QuickBooks Online: a popular accounting software choice for growing shops
QuickBooks Online is widely used for a reason: it’s a solid all-around accounting software option for many small businesses, especially when you’re juggling multiple accounts, sales channels, or team members.
If you’re a retail store or online seller, QuickBooks Online tends to work well when you want:
Strong bank connections and reconciliation workflows
Customizable reporting (especially once your chart of accounts is clean)
A big ecosystem of integrations (POS, ecommerce, payment processors)
Room to grow without switching platforms every year
Where shop owners get tripped up is not usually the tool. It’s the setup.
A messy chart of accounts, uncategorized transactions, and mismatched deposits can make QuickBooks feel “wrong,” even when it’s technically fine.
For more info on what “caught up” actually looks like month to month, this post lays it out in plain English: When To Move From DIY Bookkeeping To Professional Support
And if your goal is better cash flow decisions (not just prettier reports), you’ll want this one too: Cash Flow Mistakes (And What To Do Instead)
Xero: flexible accounting software with clean reporting
Xero is another cloud-based accounting software option I like, especially for business owners who want clean reporting, easy collaboration, and a system that feels less cluttered.
In plain terms, Xero can be a great fit if you:
Want a straightforward dashboard and reports
Work with a bookkeeper who prefers Xero workflows
Like a simpler, cleaner user experience
Want strong bank reconciliation tools
One thing I like about Xero is how it supports a calm monthly routine. When your reconciliation habits are consistent, your reports stop being “surprise math.”
Just like QuickBooks, Xero works best when your workflow is built around how your business runs.
That means thinking through things like: sales channels, inventory approach, sales tax, and how you want owner pay to flow.
If taxes are part of what’s driving your software decision, this guide helps you build a simple system for setting money aside: Estimated Tax Payments: How Much to Set Aside
FreshBooks, Wave, and other accounting software options to know
Not every business needs the biggest, most robust accounting software on day one.
Sometimes you need “simple and consistent” more than “every feature under the sun.”
FreshBooks is often a better fit for service-based businesses that live and die by invoicing and client billing. If you sell products plus services (like workshops, consulting, or subscriptions), it can still be worth a look, but it’s usually strongest for invoice-heavy businesses.
Wave can be a helpful starting place if you’re very small, very simple, and cost is the main driver. The tradeoff is that you may outgrow it faster once you add sales channels, inventory, payroll, or more detailed reporting needs.
A few other accounting software options you might hear about:
Zoho Books: Often appealing if you already use Zoho tools
Sage: A long-time player with different product levels
NetSuite or other ERPs: More for larger, complex operations (usually past the “DIY but overwhelmed” stage)
My general rule: if your business has inventory, multiple sales channels, or sales tax across states, pick accounting software that can grow with those realities.
And no matter what you choose, remember this: your ecommerce platform or POS is not your accounting system. Shopify and Square are amazing at selling. Your accounting software is where you prove what you earned, what it cost, and what you keep.
For more info on keeping records in a way that supports tax time (and reduces panic), this IRS resource is worth bookmarking: IRS recordkeeping guidance
Quick wins: make your accounting software easier (and switch safely if needed)
Before you switch accounting software, I always like to grab the “low effort, high payoff” improvements first.
Quick wins
Reconcile every month (even if it’s not perfect, make it consistent).
Separate business and personal spending as much as possible.
Use consistent categories (stop creating a new expense account every Tuesday).
Track processing fees in a repeatable way (Stripe, Shopify, Square, PayPal).
Set a weekly 20-minute “money reset” to review transactions and receipts.
A simple numbers example (why this matters)
Let’s say your online store does $20,000/month in sales.
If processing fees average 2.9% + $0.30, you might easily pay around $600 in fees (give or take) depending on order volume and platforms.
If your accounting software setup is not tracking fees correctly, your reports can overstate profitability. That can lead to pricing decisions that feel fine, but quietly squeeze your margin.
This is why “good enough bookkeeping” often stops being good enough as you grow.
If this sounds like you…
You dread logging in because you know it’s messy.
Deposits don’t match sales, and you don’t know why.
You are behind, and you keep telling yourself you’ll catch up “next week.”
You want clean reports, but you also want your evenings back.
You are not failing. Your system just needs a better plan.
Accounting software switch checklist
Balanced Path Tip
If you are switching because your current system feels chaotic, don’t copy the chaos into the new tool. Use the switch as a reset: fewer categories, cleaner workflows, and a monthly routine you can actually keep.
If you want help building that routine, this is where my setup work fits best: Bookkeeping Set Up Services
When it’s time to bring in bookkeeping help
There’s a point where the best accounting software won’t fix the real problem: you’re doing too much, too often, with too little time.
Here are the moments I see most often when it’s time to get support:
You’re behind more than one month, and it keeps snowballing
You don’t trust your Profit & Loss, so you avoid looking
Sales tax, inventory, or multiple platforms have added complexity
You’re preparing for taxes, funding, or hiring and need clean numbers
You feel like bookkeeping is stealing your energy from the work that actually makes money
If you want ongoing support that keeps things current and calm, start here: Bookkeeping services
If the pressure point is tax season (or you want to stop guessing), here’s the path for that: Tax services
And if the stress is bigger than the business numbers alone, I also help with the personal side so paychecks and savings feel steadier: Personal finance services
Key Takeaways
The best accounting software is the one that matches how you sell and how you want to operate.
QuickBooks Online and Xero are strong choices for many retail and online sellers, but setup matters more than brand.
FreshBooks and Wave can work for simpler businesses, but many product-based sellers outgrow them.
Reconciliation and fee tracking are the two biggest “make or break” habits for accurate reports.
If bookkeeping is taking over your life, it’s okay to upgrade your support, not just your software.
Quick Links
Visit the Balanced Path Resource Library for downloadable resources.
FAQs
What is the best accounting software for a small retail store?
For many retail stores, QuickBooks Online or Xero are strong choices because they handle bank reconciliation, reporting, and integrations well. The best pick depends on your POS, inventory needs, and how many sales channels you run.
Is QuickBooks Online or Xero better for online sellers?
Either can work well, but the better option is usually the one that integrates cleanly with your ecommerce platform and creates consistent deposits and fee tracking. If your setup is messy, the “better” platform won’t feel better until the workflow is fixed.
Do I need accounting software if I sell on Shopify or use Square?
Yes. Shopify and Square track sales activity, but accounting software tracks profitability, expenses, and what you can deduct at tax time. Think of your selling platform as the cash register, and your accounting software as the full financial story.
When should I switch accounting software?
Switch when your current system no longer fits your business, you’re adding complexity (inventory, staff, sales channels), or your reports are unreliable. The smoothest time is usually the start of a month or quarter, after you’ve reconciled.
What’s the easiest accounting software for beginners?
If you want beginner-friendly and scalable, QuickBooks Online and Xero are both popular. The easiest tool is the one that’s set up correctly with a simple chart of accounts and a monthly routine you’ll actually follow.
Conclusion
The right accounting software can save you time, reduce errors, and help you make decisions without second-guessing. Whether you choose QuickBooks Online, Xero, or a simpler option, the real win comes from a clean setup and a consistent monthly routine.
If you want help choosing, switching, or cleaning up what you already have:
Email me at [email protected]
Call/text 603-892-8879
Or book an introduction call.
