The Best Bookkeeping Software for Your Houston Business in 2025

I see this problem every week in my office. Business owners come in stressed because they’ve watched QuickBooks demos, read Xero reviews, talked to their buddy about Wave, and now they’re more confused than when they started.

Here’s what I always tell them. The best software is the one you’ll actually use. I had a contractor from Sugar Land pay $2,400 a year for advanced features he never touched once. Same month I had a freelancer in Midtown using free software with perfectly organized books because she logged in every Friday morning without fail.

What Most Houston Businesses Should Use

I recommend QuickBooks Online to most of my clients. Not because it’s perfect. It’s definitely not. But here’s why I push it. Your CPA already knows it cold. Everything else in your business connects to it. You won’t outgrow it in two years like you might with something simpler.

That said, safe doesn’t always mean right. Let me walk you through the real situations where other options actually make sense.

QuickBooks Online: What 8 Out of 10 Clients Use

About 80% of the tax returns that land on my desk are using QuickBooks. That’s not a coincidence. When you’re that common, good things happen.

What it costs in 2025:

• Simple Start: $29/month (1 user)
• Essentials: $59/month (3 users)
• Plus: $89/month (5 users)
• Advanced: $199/month (25 users)

Keep an eye out for their promotions. I see 50% off the first three months pretty often. Worth waiting for if you’re not in a rush.

Why I Recommend QuickBooks

I know it inside and out. When you send me your file in March, I don’t have to learn a new system. I go straight into your books, find the problems, fix them, and get your return filed. That saves you money on the tax work.

Everything in your business plugs into it. I have a restaurant client in Montrose running Toast on her POS, Square for online orders, and Gusto for payroll. All three sync to QuickBooks with no manual work. She used to spend 3 hours on reconciliation. Now it takes her 15 minutes.

It actually grows with you properly. I’ve watched clients start at Simple Start for $348 a year when they’re solo. When they add inventory they move to Plus at $1,068. Then they hit Advanced at $2,388 when they need custom reports and multiple users. The data follows you cleanly every single time.

Where QuickBooks Annoys Me

The pricing is designed to trap you. You start at $29/month thinking that’s all you need. Then you realize you need bill payment and jump to $59. Want project tracking? You’re at $89. They deliberately lock basic stuff behind higher tiers.

Their support is weak. You’ll wait forever on hold. When someone finally answers they clearly don’t know accounting. Half my clients just text me instead of wasting time with QuickBooks support.

It’s not user friendly. I’ve been using it for over a decade and I still search for features sometimes. New people get lost in it fast.

Who Should Use QuickBooks

Use it if you’re working with an outside accountant like us. Use it if you plan to run payroll through the software. Use it if you need everything to connect smoothly. Use it if you want something proven and stable instead of the latest trends.

Xero: The QuickBooks Alternative

About 15% of my clients run Xero. It’s the real alternative to QuickBooks, and some people absolutely love it.

What it costs in 2025:

• Starter: $15/month (limited transactions)
• Standard: $42/month (most features)
• Premium: $78/month (everything)

Why Some Clients Pick Xero

Unlimited users on every single plan. I worked with a marketing agency in River Oaks with 7 people who needed access. On QuickBooks Advanced they’d spend $2,388 a year. On Xero Standard they spend $504 a year. That’s $1,884 staying in their pocket.

The design is cleaner. It feels modern. Not cluttered like QuickBooks can feel. People who got lost in QuickBooks usually prefer how Xero looks and works.

Bank reconciliation actually works better. Their matching algorithm is smarter. The workflow makes sense. This is the one place Xero clearly wins.

Where Xero Causes Problems

Most Houston CPAs don’t know it. I know it because I have clients using it. Some local accountants will charge you extra if you use Xero because they have to spend time learning it.

No built-in payroll. QuickBooks has payroll included. Xero makes you use Gusto or someone else. That’s another login, another company to deal with, another connection to keep working.

Industry features don’t go as deep. My construction and manufacturing clients need things QuickBooks has that Xero doesn’t cover.

Who Should Use Xero

Use it if you have multiple team members who need access and want to save money. Use it if you tried QuickBooks and couldn’t stand it. Use it if you do business internationally and need multi-currency. Use it if you care about good design and how the interface feels.

Wave: Totally Free (But With Real Limits)

Wave is free. Completely free. No credit card. No trial period ending. I recommend it to one specific group of people.

What it costs:

• Accounting software: $0
• Payment processing: 2.9% plus $0.60 per transaction
• Payroll: $40/month base plus $6 per employee

They make money when you use their payment processor. The accounting software is their way to get you in the door.

Why Wave Works for Some People

It’s free. A freelancer in Midtown just getting started can track money in and out without paying anything monthly. That matters when you’re living on fumes and every dollar counts.

It’s simple. Not many features means not much confusion. If you just need to track basic income and expenses, it works.

Receipt scanning is included. You can upload unlimited receipts at no cost. Other software charges extra for this.

Why I Don’t Recommend Wave Long Term

Nothing connects to it. Once you add other tools to your business, Wave sits by itself. No automatic connections. You’re doing everything by hand.

You’ll outgrow it fast. Add inventory, job costing, or anything complicated and Wave breaks. Then you’re switching mid-year and that’s a pain.

Support doesn’t really exist. Free software gets free support. You’re on your own.

Who Should Use Wave

Solo freelancers and consultants with simple businesses. People who have zero budget for software. Service businesses with no inventory to track. Anyone who knows they’ll switch to real software within a year or two anyway.

FreshBooks: For Service Businesses That Bill Hourly

FreshBooks started as invoicing software and tacked on accounting later. If collecting payments from clients is your biggest nightmare, FreshBooks is worth a look.

What it costs in 2025:

• Lite: $19/month (5 billable clients)
• Plus: $33/month (50 clients)
• Premium: $60/month (500 clients)

What FreshBooks Does Really Well

Invoicing is fast. I have an IT consultant in the Galleria who bills 30 clients a month. He creates an invoice in about 90 seconds. Automatic reminders go out. Clients can pay online. They see their own portal.

Time tracking is built in. If you bill hourly you track time in the app and turn it into an invoice instantly. No typing everything twice.

The phone app actually works. You photograph receipts, send invoices, see who paid you, all from your phone without wanting to break it.

Where FreshBooks Falls Short

Client limits on the cheap plans. The $228 a year plan only lets you bill 5 clients. A growing agency hits that limit fast.

It’s not real accounting. FreshBooks doesn’t use standard double-entry bookkeeping by default. That makes my job harder when I’m doing your taxes.

It doesn’t work for product businesses. No inventory. No manufacturing. This is pure service business software.

Who Should Use FreshBooks

Use it if you’re a freelancer who bills by the hour. Use it if you run a service agency. Use it if you’re a consultant with a lot of clients. Use it if getting paid matters more than complex accounting.

Zoho Books: Only If You’re Already Using Zoho

I only push Zoho Books if you’re already using Zoho for other stuff.

What it costs in 2025:

• Free tier: Up to $50,000 annual revenue
• Standard: $15/month
• Professional: $40/month
• Premium: $60/month

Why Zoho Can Make Sense

It plugs into other Zoho products. I know a sales team in West University using Zoho CRM. Their customer data flows straight into Zoho Books automatically. No middle layers. No sync problems.

Automation is powerful here. More workflow options than you get elsewhere. If you’re technical you can build some impressive stuff.

You get good features for the price. Inventory, multi-currency, project tracking. Stuff that costs extra on other platforms.

Why I Don’t Recommend Zoho Often

Bank connections aren’t reliable. Links to US banks drop more than they do on QuickBooks. You end up manually importing transactions.

Not many accountants know it. Not many tutorials. Getting help takes longer.

It only works well if you’re using the whole Zoho suite. By itself it’s just okay. If you’re not using Zoho CRM and Zoho Projects, get something else.

Who Should Use Zoho

Use it if you’re already using other Zoho products. Use it if you do business internationally. Use it if you need features but hate spending money. Use it if you have someone on your team who’s technical and can set it up right.

QuickBooks vs. Xero: The Real Decision

For most growing Houston businesses, it comes down to these two.

What Matters	QuickBooks Online	Xero
Mid-tier price	$59/month	$42/month
Users included	3	Unlimited
Your CPA knows it	Probably yes	Maybe not
Payroll	Built in	Third party required
Learning curve	Moderate	Moderate

Pick QuickBooks if your accountant really prefers it (I do), you want payroll built in, or you need everything to plug in together.

Pick Xero if you have 5 or more people who need access, the $17/month difference matters at your size, or you like clean modern interfaces.

Before You Commit to Anything

Ask your CPA what they prefer. If you work with an outside accountant, find out what they like. Using their preferred software saves you money and frustration. I charge less for QuickBooks files because I work faster with them.

Think ahead 3 years. Switching accounting systems in the middle of the year is painful and expensive. Pick something that fits where you are now plus where you want to be in 2028.

Actually test it before you decide. All of these have free trials. Don’t just watch the demo. Import some real transactions. Reconcile your actual bank account. Run the actual reports you need.

What Actually Matters

The real differences between these platforms are smaller than their marketing makes it sound.

They all track money in and money out. They all connect to your bank. They all make reports. They all have things that drive you crazy.

What really matters is whether you’ll actually use it. I have clients using Wave with perfect books because they sit down every Friday morning and reconcile. I have clients who spent money on QuickBooks Advanced and never logged back in after the first day.

The software is just the tool. Your habits are what make your books clean.

---

Need help choosing bookkeeping software or setting it up properly? We help Houston businesses pick the right platform and configure it correctly from day one. Contact us and let’s talk through your specific situation.