Best Bookkeeping Software for Multiple Businesses

Managing bookkeeping for multiple businesses can quickly get overwhelming if you don’t have the right tools. Whether you run a group of companies, a franchise, or several side businesses, you need software that’s robust enough to handle multiple accounts, easy enough to manage everything in one place, and scalable as your businesses grow.

Here’s the breakdown of the best bookkeeping software for managing multiple businesses, starting with a versatile favorite, FreshBooks.

1. FreshBooks

FreshBooks isn’t just for freelancers and small businesses anymore; it’s now powerful enough to handle multiple businesses under one account. I’ve seen business owners with multiple streams of income use FreshBooks to manage their different ventures without a hitch. Its intuitive interface makes it easy to switch between businesses while keeping all financial records organized.

Key Features:

  • Multiple Businesses Setup: FreshBooks allows you to create and manage separate accounts for each of your businesses.
  • Expense Tracking: Easily track and categorize expenses for each business individually.
  • Invoicing: Create customized invoices for each business with different branding and details.
  • Reports: Generate reports like profit/loss, balance sheets, and expense summaries per business.

Why It Works:

FreshBooks is the go-to for businesses that want to keep things simple and organized. Its multi-business feature is user-friendly, and switching between businesses is seamless. Whether you’re running a small side hustle or managing multiple companies, FreshBooks gives you clarity and control without a steep learning curve.


2. QuickBooks Online (Advanced)

QuickBooks is one of the most powerful accounting software options available, and it’s especially strong for managing multiple businesses. When I helped a client with several franchises implement QuickBooks, they were able to streamline all their financial operations under one system, saving time and reducing errors.

Key Features:

  • Multiple Business Management: You can manage multiple companies under the same account but still keep their financials separate.
  • Custom Reporting: Generate separate reports for each business, or create consolidated reports for a bird’s-eye view.
  • Automation: Automate recurring tasks like invoicing, payroll, and payment tracking across all businesses.
  • Third-Party Integrations: Works well with apps like PayPal, Shopify, or CRMs to manage business operations and sync financial data.

Why It Works:

QuickBooks Online (Advanced) is excellent for more complex needs, like when your businesses are scaling or have a large volume of transactions. Its ability to integrate with other software makes it ideal for businesses with varying operational needs, whether it’s retail, service, or e-commerce.


3. Xero

Xero is a cloud-based accounting software known for its flexibility and ability to manage multiple businesses. A small business owner I know uses Xero to track her online store and a separate consulting firm without needing separate subscriptions for each. It provides a neat and simple interface for handling multiple ventures.

Key Features:

  • Multiple Business Dashboards: View and manage multiple businesses from a single dashboard.
  • Expense and Inventory Tracking: Ideal for businesses that need to track expenses and inventory for each entity.
  • Invoicing & Payments: Easily send invoices and accept payments for different businesses under one account.
  • Bank Reconciliation: Connect multiple bank accounts for different businesses and reconcile transactions smoothly.

Why It Works:

Xero is great for business owners who want to manage several companies from one unified account. It’s also a great choice for businesses with complex inventory needs or those in industries where managing cash flow is critical.


4. Zoho Books

Zoho Books is part of the Zoho suite, making it an attractive option for entrepreneurs already using Zoho’s other business tools like CRM or project management. A colleague running multiple small online businesses uses Zoho Books to keep track of separate finances while benefiting from the integrations within Zoho’s ecosystem.

Key Features:

  • Multi-Organization Setup: Set up separate accounts for each business and manage them all from one interface.
  • Custom Invoicing: Customize invoices for each business, including different currencies and tax settings if needed.
  • Integrated Business Tools: Works seamlessly with other Zoho apps, like Zoho CRM, to handle everything from sales to customer support.
  • Expense Tracking: Track expenses by business, making it easy to see where each company is spending and earning.

Why It Works:

Zoho Books is an ideal solution for small to medium businesses that need strong integration with other Zoho business tools. It’s also excellent for entrepreneurs managing global businesses, as Zoho handles multi-currency and tax complexities with ease.


5. Wave Accounting

Wave is a free accounting solution that’s perfect for managing multiple businesses, especially if you’re just starting out. I’ve recommended Wave to small business owners juggling multiple ventures without large budgets for accounting software.

Key Features:

  • Unlimited Business Accounts: Set up and manage unlimited businesses under one Wave account.
  • Invoicing: Send customized invoices for each business and track payments.
  • Expense Management: Track and categorize expenses for each business separately.
  • Payroll Integration: Manage payroll for different businesses under the same platform.

Why It Works:

Wave’s free pricing makes it the perfect option for startups and small business owners looking for basic accounting features. It’s not as feature-rich as some of the paid options, but it’s more than enough if you’re looking for something simple and cost-effective.


6. Sage Business Cloud Accounting

Sage offers a robust solution for managing multiple businesses, particularly for those who need more advanced features like inventory tracking and global accounting. A mid-sized company I worked with used Sage to track their domestic and international operations under one account.

Key Features:

  • Multiple Companies: Manage multiple businesses from a single Sage account.
  • Global Accounting: Handle different tax regulations, currencies, and reporting standards for businesses operating internationally.
  • Inventory Management: Sage offers detailed inventory tracking, making it ideal for businesses that deal with physical products.
  • Advanced Reporting: Generate custom reports for each business or a consolidated overview.

Why It Works:

Sage Business Cloud is excellent for businesses that need to manage global operations and inventory, offering a more sophisticated toolset than some of the simpler accounting software. It’s ideal for medium to large companies with complex bookkeeping needs.


Things to Consider When Managing Multiple Businesses

1. Separation of Financials

Make sure the software allows you to manage each business’s finances separately, even though you may be using a single platform. This includes separate reporting, invoicing, and bank reconciliation.

2. Ease of Switching Between Businesses

The ability to quickly switch between businesses without logging out or navigating complex menus will save you time and reduce errors.

3. Scalability

As your businesses grow, your software should grow with you. Look for solutions that offer additional features like payroll, inventory management, and automation as you expand.

4. Reporting

Make sure your bookkeeping software can generate individual reports for each business while also giving you a consolidated view if necessary. This is especially important when presenting financials to stakeholders.


Comparison Table for Quick Review

Software Best For Key Features Price Range
FreshBooks Small to medium businesses Multiple business setup, invoicing, expense tracking Starts at $15/month
QuickBooks Larger businesses with complex needs Fund accounting, custom reporting, automation $30+/month
Xero Growing businesses Multiple dashboards, inventory management, reporting $13+/month
Zoho Books Small to medium global businesses Multi-organization setup, integration with Zoho apps Starts at $15/month
Wave Startups, side businesses Free accounting, invoicing, payroll Free
Sage Business International operations Global accounting, inventory management, reporting $10+/month

My Top Recommendation

For businesses with straightforward needs, FreshBooks is a great choice thanks to its ease of use and cost-effective pricing. If you’re managing more complex financial operations, such as franchises or businesses across multiple countries, QuickBooks Online (Advanced) or Sage Business Cloud will provide the power and flexibility you need.

If you’re just starting out with smaller ventures, Wave is an excellent free solution to keep costs down while still maintaining proper financial records.

The best software for managing multiple businesses will depend on your current needs and the growth you anticipate. Try a few out with free trials, and choose the one that fits best!

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