Best QuickBooks for Small Business with Payroll: Streamline Your Finances

A Comprehensive Guide to Finding the Perfect QuickBooks Solution for Your Small Business

Are you a small business owner looking for a user-friendly accounting software with payroll management capabilities? Look no further than QuickBooks! In this article, we will explore the best QuickBooks options specifically designed for small businesses with integrated payroll features. Streamline your financial processes and simplify payroll tasks with ease.


You may have heard of QuickBooks before, but did you know that it offers specialized versions tailored to meet the unique needs of small businesses? Whether you’re a solopreneur or have a small team, QuickBooks can provide you with the tools to effectively manage your finances and payroll.

With its user-friendly interface, extensive features, and powerful integrations, QuickBooks has become the go-to accounting software for small businesses. It allows you to track your income and expenses, generate professional invoices, manage inventory, and even calculate and file taxes seamlessly.

In this guide, we will explore seven of the best QuickBooks options for small businesses with payroll capabilities. From self-employed individuals to small teams, there is a QuickBooks solution suitable for every type of business.

QuickBooks Online

“QuickBooks Online is the top choice for small businesses that value flexibility and accessibility. With cloud-based functionality, you can access your financial data anytime, anywhere.” – Small Business Trends

QuickBooks Online is the cloud-based version of QuickBooks, allowing you to access your financial data from any device with an internet connection. It offers robust payroll features that enable you to automate payroll calculations, pay employees with direct deposit, and even file taxes effortlessly.


With QuickBooks Online, you can:

  1. Track income and expenses in real-time
  2. Generate professional invoices and accept online payments
  3. Manage inventory and track sales
  4. Automate payroll calculations, tax deductions, and payments
  5. Access your financial data securely from any device
  6. Integrate with other business tools for seamless workflows
  7. Make informed business decisions with insightful reports

Getting Started with QuickBooks Online

Getting started with QuickBooks Online is a straightforward process. Here’s a step-by-step guide to help you set up your account:

  1. Step 1: Sign up for QuickBooks Online
  2. Visit the QuickBooks website and sign up for an account. You can choose from different plans based on your business needs.

  3. Step 2: Set up your company information
  4. Enter your business name, contact details, and tax information. This information will be used to customize your QuickBooks experience.

  5. Step 3: Customize your chart of accounts
  6. A chart of accounts is a list of categories where you classify your income and expenses. Customize it to accurately reflect your business structure.

  7. Step 4: Connect your bank accounts and credit cards
  8. Link your bank accounts and credit cards to QuickBooks Online. This will allow you to automatically import transactions, saving you time and reducing manual data entry.

  9. Step 5: Set up payroll
  10. Enter your employees’ information, such as their names, addresses, and pay rates. QuickBooks Online will calculate payroll taxes and deductions automatically.

  11. Step 6: Run payroll
  12. Once you have set up your payroll, you can run it with just a few clicks. QuickBooks Online will generate paychecks and pay your employees using direct deposit or printed checks.

  13. Step 7: Explore other features
  14. Take advantage of QuickBooks Online’s other features, such as tracking inventory, creating invoices, and generating insightful reports. The software is designed to help you manage your business finances effectively.

QuickBooks Desktop

“QuickBooks Desktop offers advanced features and robust functionality, making it a popular choice for small businesses with more complex accounting needs.” – Forbes

QuickBooks Desktop is the traditional software version of QuickBooks, installed directly on your computer. It provides enhanced features and capabilities, making it suitable for businesses that require more advanced accounting tools.


With QuickBooks Desktop, you can:

  1. Manage and track inventory efficiently
  2. Create customized sales orders, purchase orders, and invoices
  3. Generate comprehensive financial reports and forecasts
  4. Process and track payroll accurately
  5. Automate recurring transactions
  6. Utilize batch invoicing and advanced pricing options
  7. Customize your software with industry-specific add-ons

Getting Started with QuickBooks Desktop

Setting up QuickBooks Desktop requires a few additional steps compared to QuickBooks Online. Follow this guide to get started:

  1. Step 1: Purchase and install QuickBooks Desktop
  2. Visit the QuickBooks website or authorized resellers to purchase the software. Once purchased, follow the installation instructions to set it up on your computer.

  3. Step 2: Set up your company file
  4. When you first launch QuickBooks Desktop, you’ll be prompted to create a new company file. Enter your business information, such as your name, address, and tax details.

  5. Step 3: Customize your preferences
  6. Explore the preferences and settings options in QuickBooks Desktop to tailor the software to your specific needs. You can customize features like invoice templates, payment terms, and report layouts.

  7. Step 4: Import your financial data
  8. If you are transitioning from another accounting system or spreadsheet, you can import your financial data into QuickBooks Desktop. This will save you from manually entering historical data.

  9. Step 5: Set up payroll
  10. Similar to QuickBooks Online, you need to enter your employees’ information and set up payroll taxes and deductions. QuickBooks Desktop offers various payroll options to fit your unique requirements.

  11. Step 6: Process payroll
  12. Once your payroll is set up, you can easily process it within QuickBooks Desktop. The software will calculate wages, taxes, and deductions, and generate paychecks or direct deposit files.

  13. Step 7: Explore additional features
  14. QuickBooks Desktop offers an array of advanced features, such as inventory tracking, job costing, and custom reporting. Familiarize yourself with these features to maximize the efficiency of your accounting processes.

QuickBooks Self-Employed

“QuickBooks Self-Employed is the perfect solution for freelancers and independent contractors who need to manage their finances and track business expenses effortlessly.” – Entrepreneur

QuickBooks Self-Employed is specifically designed for self-employed individuals who need a simple yet effective way to manage their finances. It offers essential accounting tools and allows you to separate personal and business expenses easily.


With QuickBooks Self-Employed, you can:

  1. Track and categorize business income and expenses
  2. Automatically import transactions from linked bank accounts and credit cards
  3. Estimate quarterly taxes and simplify tax preparation
  4. Create and send professional invoices on the go
  5. Maximize deductions by capturing receipts and mileage
  6. Generate insightful reports for a clear overview of your business
  7. Access your financial data from any device with the mobile app

Getting Started with QuickBooks Self-Employed

Setting up QuickBooks Self-Employed is quick and easy. Here’s how you can get started:

  1. Step 1: Sign up for QuickBooks Self-Employed
  2. Visit the QuickBooks website and sign up for a QuickBooks Self-Employed account. Choose the plan that suits your needs and budget.

  3. Step 2: Connect your bank accounts and credit cards
  4. Link your personal and business bank accounts and credit cards to QuickBooks Self-Employed. This allows the software to automatically import your transactions.

  5. Step 3: Categorize your income and expenses
  6. Review and categorize your income and expenses to accurately track your business finances. QuickBooks Self-Employed learns from your categorizations and becomes more accurate over time.

  7. Step 4: Track mileage and capture receipts
  8. Use the QuickBooks Self-Employed mobile app to track your mileage automatically. You can also capture receipts by taking pictures with your phone and attaching them to expenses.

  9. Step 5: Estimate and pay quarterly taxes
  10. QuickBooks Self-Employed provides estimates for your quarterly tax payments based on your income and expenses. It helps you stay organized and prepared for tax season.

  11. Step 6: Generate professional invoices
  12. Create and send professional invoices to your clients directly from the QuickBooks Self-Employed app. You can easily track invoice status and get paid faster.

  13. Step 7: Review insightful reports
  14. Utilize the reporting features in QuickBooks Self-Employed to gain valuable insights into your business’s financial health. Track your profit and loss, see your top expenses, and monitor your tax obligations.

FAQ – Best QuickBooks for Small Business with Payroll

1. Can I upgrade my QuickBooks plan as my business grows?

Yes, QuickBooks offers easy plan upgrades to accommodate the changing needs of your growing business. You can seamlessly transition to a higher plan to access additional features and increased usage limits.

2. Can I integrate QuickBooks with other business tools?

Absolutely! QuickBooks provides integrations with various apps and services to streamline your workflows and improve efficiency. From CRM software to payment processors, you can connect QuickBooks with the tools you already use.

3. Can I access QuickBooks Online from my mobile device?

Yes, QuickBooks Online has a user-friendly mobile app available for iOS and Android devices. With the app, you can access your financial data, send invoices, track expenses, and even run payroll on the go.

4. Are there any additional fees for using QuickBooks Payroll?

Yes, QuickBooks Payroll has additional fees based on the number of employees you have and the payroll features you choose. You’ll need to subscribe to a payroll plan that suits your business needs and pays the corresponding monthly fee.

5. Can I try QuickBooks before committing to a paid plan?

Yes, QuickBooks offers a free trial period for you to test out the software and its features. It allows you to explore the functionalities and determine if it’s the right fit for your business before making any financial commitments.

6. Is QuickBooks Desktop compatible with Mac computers?

Yes, QuickBooks Desktop is available for both Windows and Mac operating systems. You can choose the version that matches your computer’s operating system and enjoy the same powerful features and functionality.

7. How secure is my financial data with QuickBooks?

QuickBooks takes data security seriously and employs advanced encryption and secure servers to protect your information. Your financial data is encrypted during transmission and stored on secure servers, ensuring the confidentiality and integrity of your sensitive data.

Summary of Main Points

After exploring the different QuickBooks options for small businesses with payroll, here are the key takeaways:

  1. QuickBooks Online offers flexibility and accessibility with cloud-based functionality.
  2. QuickBooks Desktop provides advanced features and robust functionality for more complex accounting needs.
  3. QuickBooks Self-Employed is perfect for freelancers and independent contractors.
  4. You can upgrade your QuickBooks plan as your business grows.
  5. Integrate QuickBooks with other business tools to streamline workflows.
  6. Access QuickBooks Online from your mobile device with the mobile app.
  7. Review additional fees for using QuickBooks Payroll based on your business needs.


Choosing the best QuickBooks solution for your small business with payroll capabilities is vital in streamlining your financial management and simplifying payroll tasks. Whether you opt for QuickBooks Online, QuickBooks Desktop, or QuickBooks Self-Employed, you can expect to save time, improve accuracy, and gain valuable insights into your business’s financial health. Take the first step towards financial success by adopting the best QuickBooks solution for your small business today.

Disclaimer: The information provided in this article is for general informational purposes only and should not be construed as professional advice. Consult with a qualified accounting professional before making any financial decisions.

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