The right accounting software can save you hours each week by automating invoicing, tracking expenses, and simplifying tax prep. My top pick is QuickBooks Online because it covers all the essentials, adapts as your business grows, and is backed by a huge network of accounting pros. Tools like that give you real-time visibility into your finances without needing to hire staff or outsource everything.

With that in mind, here are my top five self-employed accounting software:

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  • Track income and expenses with precision using built-in smart categorization.
  • Easily generate tax-ready reports and manage quarterly filings.
  • Integrate seamlessly with your existing tools and bank accounts.
  • Enjoy support and flexibility tailored to businesses at every stage.
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TL;DR for self-employed individuals

  • For a general-purpose tool with full accounting features, pick QuickBooks Online because it’s versatile, scalable, and widely supported.
  • For a product-based business or one with plans to grow, pick Zoho Books as it offers robust inventory, automation, and long-term scalability at a competitive price.
  • For those on a tight budget needing just the basics, choose Wave since it handles income and expense tracking well at little to no cost.
  • For freelancers focused on invoicing and client work and without plans to hire, go with FreshBooks because it’s the most intuitive option with strong billing tools.
  • For bookkeepers managing multiple clients, use ZipBooks as its Accountant plan makes switching between books simple and efficient.

Why you can trust my advice

I’m a CPA with over four years of experience evaluating accounting software across various industries. I’ve tested and assessed dozens of tools through hands-on use, not just surface-level research. My background in accounting, process design, and accounting technology allows me to focus on what actually works for real users. Whether you’re a freelancer, a small business owner, or part of a growing team, my recommendations are grounded in practical insight and proven expertise.

TechnologyAdvice is able to offer our services for free because some vendors may pay us for web traffic or other sales opportunities. Our mission is to help technology buyers make better purchasing decisions, so we provide you with information for all vendors — even those that don’t pay us.

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Best self-employed accounting software comparison

My overall score

Monthly price

No. of users

Bookkeeping assistance

QuickBooks logo.
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4.7

$35 to $235

1 to 25

QuickBooks Live or ProAdvisor

Zoho Books logo
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4.6

$0 to $275

1 to 15 plus $3 monthly per added user

Zoho Advisor

Wave logo
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3.2

$0 or $16

1 or unlimited

Wave Advisor

Freshbooks logo
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3.4

1, plus $11 monthly per added user

1, plus $11 monthly per added user

N/A

Zipbooks Logo
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3.5

$0 to $35 or custom

1 to unlimited

Via ZipBooks Accountant

To identify the best self-employed accounting software, I applied a consistent rubric across essential categories that every accounting platform should address. The following includes all the platforms I initially evaluated before narrowing the list down to the top five recommendations featured in this buyer’s guide:

  • Wave
  • NCH Express
  • QuickBooks Online
  • QuickBooks Desktop
  • FreshBooks
  • Xero
  • Zoho Books
  • QuickBooks Enterprise
  • Sage 50 Accounting
  • Gnucash
  • AccountEdge

When developing the rubric for this buyer’s guide, I prioritized features that matter most to self-employed individuals, such as invoicing and banking, and assigned them greater weight in the evaluation. I also accounted for scalability by awarding extra points to providers that offer tools for long-term growth. Finally, I included an expert rating to bring subjective insights without disproportionately skewing the overall scores.

Here are the criteria I used to evaluate each software platform:

  • Pricing and value (10%): I didn’t base this score on cost alone. Instead, I evaluated both the listed pricing and the overall value delivered by the software. To balance those fairly, I used a custom transmutation table that converts raw cost and value assessments into a final score. This method prevents high-priced but feature-rich tools from being unfairly penalized while ensuring that free or low-cost platforms don’t receive inflated scores purely due to affordability.
  • Invoicing (20%): I assessed each software’s ability to create, send, and track invoices efficiently. I gave preference to tools that make invoicing intuitive and straightforward without requiring you to navigate through unnecessary steps or complex workflows.
  • Billing (10%): This criterion focused on how well the software tracks vendor bills to help you manage your financial obligations. Solutions earned bonus points if they offered built-in bill payment features, though this wasn’t required. The main focus was on whether you could stay organized and current with accounts payable.
  • Banking and reconciliation (18%): I looked for platforms that allow you to connect to bank and credit card feeds and automatically categorize transactions. I also evaluated how well the software supports both manual and automated bank reconciliations, whether it can accommodate timing differences between the bank and book records, and whether you can finalize and print reconciliation reports that clearly show outstanding transactions.
  • Inventory management (5%): I evaluated whether the solutions can track both the cost and quantity of inventory, provide real-time inventory value, and support perpetual inventory systems that automatically update COGS. Other key capabilities included viewing items on purchase orders or sales orders, adjusting for returns or shrinkage, and supporting multiple inventory valuation methods, such as Average Cost, FIFO, and LIFO.
  • Project costing and accounting (10%): I focused on whether the software can assign income, expenses, and inventory usage to specific projects. Solutions scored higher if they could generate reports showing income or loss by project, create estimates with tax options, assign those estimates to jobs, and provide a comparison between actual and estimated costs for labor and materials.
  • Financial reporting (11%): This criterion reflects the breadth and quality of financial reports available. I looked for essential reports — such as the balance sheet, profit and loss (P&L) statement, and cash flow statement — along with key operational and audit tools like the general ledger, trial balance, and aging reports. I also gave points for reports that break down income by month, customer, class, or vendor to support deeper analysis.
  • Ease of use and setup (10%): I evaluated both initial setup and ongoing ease of use. This included the ability to import beginning balances, chart of accounts, and customer/vendor lists. I looked for features like new company setup wizards, guided onboarding, customizable dashboards, and intuitive workflows, such as being able to create customers or vendors directly from transaction screens. I also considered whether you could save partially completed bank reconciliations, view real-time A/R balances, and automate invoice numbering.
  • Support (6%): This was based on the range and accessibility of help options. I gave credit for live support via phone, chat, and email, as well as 24/7 availability. I also considered the availability of user communities, self-help materials, and formal training, even if paid. Extra points were awarded to platforms offering integrated bookkeeping services, certified advisor networks, and nationwide coverage for expert support.
QuickBooks logo.

QuickBooks Online: Best overall self-employed accounting software

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Overall Score

4.7/5

Pricing and value

4.3/5

Invoicing

5/5

Billing

5/5

Banking and reconciliation

5/5

Inventory management

3.8/5

Project costing and accounting

4.6/5

Financial reporting

5/5

Ease of use and setup

4.3/5

Support

4.5/5

Why I chose QuickBooks Online

QuickBooks Online is the most versatile option for self-employed professionals across industries. It is especially popular in the US, which makes it easy to find CPAs and bookkeepers who already know the platform well. It also covers all the essential accounting features, including income and expense tracking, invoicing, and bank reconciliation, so it works well for general business needs.

It aced my assessment of invoicing, billing, and banking, which shows how well it supports the core financial needs of a self-employed business. While its inventory tools are solid, they’re not as strong as what you’d get with Zoho Books, which is my recommendation if you sell physical products.

Pros

  • Covers all core accounting needs like invoicing, expense tracking, and bank reconciliation
  • Has a strong ecosystem with a wide network of ProAdvisors and third-party app integrations
  • Scales easily if your business grows or adds contractors and employees

Cons

  • Is one of the more expensive options for self-employed users
  • Can feel bloated if you only need simple bookkeeping
  • Has inventory tools that are limited compared with other platforms, like Zoho Books

  • Simple Start: $35 for one user
  • Essentials: $65 for up to three seats
  • Plus: $99 for up to five users
  • Advanced: $235 for up to 25 seats

Limited-time offer: Get 90% off QuickBooks Online for three months if you sign up by June 30, 2025. You can also start with a 30-day free trial, which forfeits the limited-time offer.

  • Invoicing with payment tracking and automated reminders
  • Expense categorization with receipt capture
  • Bank feeds with reconciliation tools
  • Built-in reports including P&L, balance sheet, and cash flow
  • Sales tax tracking and support for multiple tax rates
  • iOS and Android mobile app for on-the-go accounting
  • Access to a wide network of certified ProAdvisors
  • Integrates with hundreds of third-party apps
  • Time tracking and basic project costing (in Plus and Advanced)
  • Inventory tracking (in Plus and Advanced)
Zoho Books logo.

Zoho Books: Best for long-term scalability

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Overall Score

4.6/5

Pricing and value

4.5/5

Invoicing

5/5

Billing

4.4/5

Banking and reconciliation

5/5

Inventory management

4.5/5

Project costing and accounting

5/5

Financial reporting

5/5

Ease of use and setup

4.1/5

Support

2.2/5

Why I chose Zoho Books

Zoho Books is an excellent option if you’re thinking ahead. It’s built for scalability, with multi-tiered plans and the ability to add users as your business grows. Since it’s part of the larger Zoho ecosystem, it integrates smoothly with tools like Zoho Inventory and Zoho CRM, making it ideal if you want everything in one place.

It scored especially high in invoicing, banking, project accounting, and reporting, which makes it a well-rounded tool even beyond basic bookkeeping. Its inventory features are also solid, making it a strong choice if you have a product-based business.

Support is where it falls short. Zoho’s bookkeeping assistance is limited because Zoho is only available in California, Texas, Florida, New York, and Illinois. If you are outside those areas or want access to a broader pool of accountants and bookkeepers, QuickBooks Online is the safer pick.

Pros

  • Is great for scalability with tiered pricing and multi-user access
  • Offers a strong feature set for invoicing, banking, reporting, and project accounting
  • Provides better inventory management than most competitors at this price point

Cons

  • Offers limited bookkeeping support
  • Has few integrations with third-party tools, unless you use a third-party connector
  • Presents a steep learning curve for first-time users during setup and navigation

  • Free: $0 for one seat
  • Standard: $20 for three users
  • Professional: $50 for five seats (my recommendation for most companies)
  • Premium: $70 for 10 users
  • Elite: $150 for 10 seats
  • Ultimate: $275 for 15 users

Additional users can be added to any plan for $3 per seat, per month.

  • Invoicing with automation, customization, and client portal access
  • Expense tracking with billable expenses and receipt uploads
  • Bank feeds and smart reconciliation suggestions
  • Strong inventory tracking with reorder levels and item grouping
  • Time tracking and full project accounting tools
  • Built-in financial reports with scheduling and customization
  • Workflow automation for recurring tasks and approvals
  • Integration with Zoho apps like CRM, Inventory, and Analytics
  • Multi-user access with role-based permissions
  • Mobile app for iOS and Android
Wave logo.

Wave: Most affordable paid software

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Overall Score

3.2/5

Pricing and value

4.5/5

Invoicing

4.2/5

Billing

4.4/5

Banking and reconciliation

3.0/5

Inventory management

N/A

Project costing and accounting

1.2/5

Financial reporting

3.6/5

Ease of use and setup

2.9/5

Support

1.6/5

Why I chose Wave

Wave is one of the best self-employed accounting software programs, especially if you need essential accounting features without the high cost. Its paid plan is affordable and includes unlimited seats, which is a rare benefit for freelancers or solo business owners who collaborate with others. It does a great job with income and expense tracking, making it easy to stay on top of daily finances.

That said, Wave isn’t built for scaling. If your business is growing or planning to hire employees or manage inventory, it may fall short. It also lacks inventory features, limiting it to service-based businesses. It also underperformed in project costing and accounting because it only offers basic features. And if you’re looking for access to more bookkeepers, Wave’s network is limited, as reflected in its low support score. 

In those cases, I recommend Zoho Books because it offers more flexibility for long-term growth while still being reasonably priced. And if you need a wide network of bookkeepers, QuickBooks Online is my recommendation.

Pros

  • Is very affordable with a generous free plan for basic accounting
  • Offers a paid plan with unlimited users at no extra cost
  • Features strong income and expense tracking with built-in invoicing tools

Cons

  • Offers limited features for scaling or handling complex needs
  • Lacks inventory management and advanced reporting
  • Has limited customer support unless you’re on a paid plan

  • Wave Starter: $0 for one user
  • Wave Pro: $16 for unlimited seats

  • Income and expense tracking
  • Customizable invoicing with recurring billing options
  • Automatic bank transaction imports
  • Basic financial reports, like P&L and balance sheet
  • Unlimited users on paid plans
  • Online payment processing for credit cards and ACH
  • Receipt scanning with the iOS and Android mobile app
  • Simple dashboard for tracking cash flow
  • Built-in payroll available (US and Canada only; has an extra fee)
Freshbooks logo.

FreshBooks: Businesses without plans to hire

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Overall Score

3.4/5

Pricing and value

3.8/5

Invoicing

5/5

Billing

4.7/5

Banking and reconciliation

1.8/5

Inventory management

N/A

Project costing and accounting

4.3/5

Financial reporting

3.9/5

Ease of use and setup

3.3/5

Support

1/5

Why I chose FreshBooks

FreshBooks is tailor-made for freelancers and solo professionals, and it’s easily the most intuitive option on this list. Its interface is clean, modern, and beginner-friendly — even if you’ve never touched accounting software. What stands out are features like polished invoicing, time tracking, and client collaboration tools. That said, the scores reflect a tradeoff between usability and accounting depth. 

It earned a perfect mark for invoicing and did well in billing and project tracking. However, its banking tools are limited, and there’s no inventory management at all. Support is also a weak spot because it doesn’t offer bookkeeping assistance, which many self-employed users may eventually need. If you need more backend features or stronger reconciliation tools, QuickBooks Online is the better fit. It handles bank feeds, rules, and reconciliation much more robustly while still being accessible to solo users.

Pros

  • Features a clean, intuitive interface that’s easy to navigate
  • Offers excellent invoicing with automatic reminders and online payments
  • Has built-in time tracking and project-based billing
  • Is great for client-facing service businesses

Cons

  • Lacks inventory management
  • Has limited reporting compared with more robust platforms like QuickBooks or Zoho Books
  • Lacks bookkeeping assistance and an advisor network

  • Lite: $21 for one user
  • Plus: $38 for one seat
  • Premium: $65 for one user
  • Select: Custom priced

Each additional seat costs $11 per month.

New customer discount: Save 50% for six months on any FreshBooks plan. That includes a 30-day money-back guarantee, so you can try it risk-free.

  • Customizable invoicing with automated reminders and online payments
  • Built-in time tracking and billable hours
  • Project tracking with team collaboration
  • Basic expense tracking and receipt capture
  • Reports include P&L and tax summaries
  • Estimates and proposals with client approval
  • Accept credit cards and ACH payments
  • Integrations with Stripe, Gusto, and other third-party tools
Zipbooks logo

ZipBooks: Best for self-employed bookkeepers

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Overall Score

3.5/5

Pricing and value

4.5/5

Invoicing

4.1/5

Billing

3.6/5

Banking and reconciliation

3.3/5

Inventory management

N/A

Project costing and accounting

3.5/5

Financial reporting

4.4/5

Ease of use and setup

3.7/5

Support

1.5/5

Why I chose ZipBooks

ZipBooks, one of the best freelancer accounting software, will work great if you are a self-employed bookkeeper or manage books for multiple clients. Its Accountant plan includes client management, account switching, and simple report sharing, making it ideal if you do bookkeeping as a service. It’s also approachable enough for non-accountants who want something a little more structured than Wave but more affordable than QuickBooks.

The scores of ZipBooks reflect solid performance in key areas. It does well in invoicing, reporting, and general usability, and it’s priced competitively for what it offers. Its biggest drawback is limited support, especially if you need help with setup or troubleshooting. If you prefer a tool with stronger customer service and onboarding help, I recommend FreshBooks, especially if you want a more guided experience.

Pros

  • Has strong reporting tools for a free or low-cost platform
  • Supports multiple clients and books in the Accountant plan
  • Features a clean, lightweight interface that’s easy to learn
  • Offers good value for solo bookkeepers or freelancers
  • Includes basic project tracking and time entries

Cons

  • Lacks inventory management
  • Provides limited customer support and onboarding help
  • Has functional but not robust banking features
  • Lacks deeper integrations, like those found in QuickBooks Online
  • Has an interface that can feel too minimal for complex workflows

  • Starter: $0 for one seat
  • Smarter: $15 for five users
  • Sophisticated: $35 for unlimited seats
  • Accountant: Custom-priced for unlimited users; plan is for accounting and bookkeeping services only

  • Invoicing with online payments and auto reminders
  • Time tracking and simple project management
  • Basic expense tracking and bank reconciliation
  • Financial reports, including P&L and balance sheet
  • Team member access with role permissions
  • Smart score insights for customer and vendor tracking
  • Free plan with core features
  • Integrations with Square, PayPal, and Gusto
  • Client management with account switching (Accountant plan)

Frequently asked questions (FAQs)

What is the easiest accounting software for self-employed beginners?

ZipBooks is the easiest to learn, especially if you’ve never used accounting software. Its interface is clean, everything is labeled clearly, and it’s built with freelancers and solo professionals in mind.

Which accounting software lets me separate business and personal expenses?

QuickBooks Online and Wave let you tag or categorize transactions as business or personal. Wave even has a built-in personal finance tracking tool, which can be useful if your accounts are mixed.

Can I manage multiple businesses with one accounting software?

Yes, but not all tools support this well. ZipBooks’s Accountant plan is a good option if you need to manage separate books under one login, but that’s only suitable for accounting firms. In QuickBooks Online, each account is designed for a single company, so if you have multiple companies, you’ll need to create a separate account for each one.

Does self-employed accounting software work on mobile?

Yes, most of the top tools offer mobile apps. FreshBooks and Zoho Books have the most polished mobile experiences, letting you send invoices, track time, and view reports from your iOS or Android phone.

Eric Gerard Ruiz Avatar
Eric Gerard Ruiz
Senior Staff Writer
Eric Gerard Ruiz, a licensed CPA in the Philippines, specializes in financial accounting and reporting (IFRS), managerial accounting, and cost accounting. He has tested and review accounting software like QuickBooks and Xero, along with other small business tools. Eric also creates free accounting resources, including manuals, spreadsheet trackers, and templates, to support small business owners.