Best Accounting Software For Intercompany Transactions

Managing finances across multiple businesses or subsidiaries can be complex, and intercompany transactions are a big part of that challenge. Keeping track of shared services, inventory swaps, and intercompany loans across legal entities isn’t easy.

Whether you’re an international company with branches in different countries or a growing business with multiple subsidiaries, choosing the right multi-entry accounting software will help you maintain accurate records and streamline operations.

Do you send and receive global payments?
Try Wise Business ->

Table of contents
Sage Intacct: Best for Automation and Scale NetSuite: The All-In-One ERP QuickBooks: Best for Simplicity and Familiarity Xero Accounting Software: Best for Small Businesses That Like Things Simple Microsoft Dynamics 365: Ideal for Microsoft-First Teams

What are intercompany transactions?

Intercompany transactions are when different divisions, subsidiaries, or entities under the same umbrella conduct business with each other.¹ These might include internal loans, shared services, inventory transfers, or management fees between branches.

The real challenge lies in making sure these transactions are properly recorded, eliminated during consolidation, and reconciled to prevent double-counting. And specialized accounting software solutions can step in to help. Multi-entity accounting helps bridge the gap by offering automated processes that traditional bookkeeping software for multiple businesses can’t handle.

Let’s take a look at a few accounting software options for intercompany transactions to help you get started.

Sage Intacct: Best for Automation and Scale

Sage Intacct stands out as one of the most comprehensive enterprise accounting software solutions for multi-entity businesses. It’s the only ERP recommended by the American Institute of Certified Public Accountants (AICPA)—and they know a thing or two about accounting software.² The platform is specifically designed for businesses juggling multiple entities and currencies. It does the heavy lifting when it comes to consolidation, eliminations, and reporting.

Why it stands out:

• Advanced multi-entry consolidation with automated elimination entries
• Customizable reporting across all entities
• Built-in intercompany transaction matching and reconciliation
• Multi-currency support with real-time exchange rates
• Project-based accounting across entities
• Works with existing approval workflows

Best for: Mid-sized to large companies with international operations or project-based businesses.

Pros: Sage Intacct goes above and beyond with its reporting capabilities, featuring over 150 pre-built financial reports, integration with other business systems, strong audit trail and compliance features, flexible chart of accounts structure for each entity, and real-time financial consolidation that keeps stakeholders informed instantly.³

What to keep in mind: The main drawbacks include higher costs compared to basic accounting solutions, more setup time, and the learning curve. If you’re a smaller team, it may be more than you need right now.

NetSuite: The All-In-One ERP

NetSuite software provides a full-scale ERP-based platform for managing intercompany transactions within a unified system. NetSuite helps companies implement best practices for intercompany accounting via features desired by both the subsidiary and parent levels, which is ideal for businesses seeking an integrated approach.

Why it stands out:

• Complete ERP functionality including CRM, inventory, and HR
• Automated intercompany eliminations and consolidations
• Multi-subsidiary management with independent books
• Global financial management with multi-currency support
• Advanced analytics and business intelligence
• Customizable dashboard for each entity

Best for: Fast-growing companies that need both accounting and operational management tools, or companies planning significant expansion.

Pros: NetSuite software’s strengths are that it provides a single platform for all business operations. Additionally, there’s a highly customizable dashboard to tailor to each business, alongside international capabilities for global operations and comprehensive reporting and analytics tools.⁴

What to keep in mind: Implementation takes time. NetSuite isn't ready out of the box—there’s a steep learning curve for users transitioning from simpler systems.

QuickBooks: Best for Simplicity and Familiarity

You’ve probably heard of QuickBooks for small business accounting, but it’s evolved since then. Now, QuickBooks offers solutions for QuickBooks intercompany transactions through its Enterprise version. It provides a more accessible entry point for companies growing into multi-entity operations.

Why it stands out:

• Multi-company file management
• Basic consolidation reporting
• User permissions for different entities
• Integration with the QuickBooks ecosystem
• Custom reporting capabilities
• Inventory management across locations
• Easy setup and familiar interface
• Lower cost than full ERP systems

Best for: Small to mid-sized businesses already using QuickBooks and branching into multi-entity territory.

Pros: QuickBooks Enterprise offers many advantages, including a familiar interface for existing QuickBooks users, lower costs compared to enterprise solutions, extensive third-party integrations, a strong support community, and easier implementation processes that get businesses up and running quickly.

What to keep in mind: The limitations include restricted advanced consolidation features, manual processes required for complex intercompany transactions, scalability limitations for larger organizations, basic multi-currency support that may not meet international needs, and limited customization options compared to enterprise solutions.

Xero Accounting Software: Best for Small Businesses That Like Things Simple

Xero accounting software keeps things clean and accessible. While it doesn’t offer native intercompany eliminations, it’s a solid option if your structure is simple and you don’t mind using third-party integrations for more advanced tasks.

Why it stands out:

• Intuitive UI with great mobile access
• Supports multiple entities (via switching orgs)
• Strong ecosystem of add-ons and apps

Best for: Small businesses with basic intercompany needs and a focus on ease of use.

What to keep in mind: No built-in elimination tools, so if your setup gets more complex, you’ll need to find a workaround or switch tools.

Microsoft Dynamics 365: Ideal for Microsoft-First Teams

Already working with Microsoft tools like Excel, Power BI, or Teams? Microsoft Dynamics 365 offers a great enterprise financial software that fits right into the Microsoft ecosystem. This solution is ideal for organizations already familiar with Microsoft products.

Why it stands out:

• Seamless integration with Office 365 and other Microsoft tools
• Advanced financial consolidation and reporting
• Multi-entry support with centralized management
• Built-in AI and machine learning capabilities
• Automated intercompany transaction processing

Best for: Businesses that are already invested in the Microsoft ecosystem and want deeper automation.

Pros: Microsoft Dynamics 365 benefits from a familiar Microsoft interface that reduces training time, powerful reporting tools, strong compliance features, and integration into the existing Microsoft infrastructure.

What to keep in mind: The downsides include a complex pricing structure that can be confusing, Microsoft expertise is needed for full utilization of features, and it could be overwhelming for smaller organisations due to its time-consuming implementation processes.

Key Features to Consider When Choosing Multi-Company Accounting Software Online

When evaluating accounting software solutions for intercompany transactions, consider these must-have features.

• Automated elimination entries: The ability to automatically identify and eliminate intercompany transactions during consolidation to prevent double-counting.
• Multi-currency support: Robust multi-currency functionality with real-time exchange rates and foreign currency translation.
• Real-time consolidation: Ability to consolidate financial results in real-time rather than waiting for month-end processes.
• Integration capabilities: Seamless integration with other business systems, including CRM, inventory management, and payroll.
• Dimensional reporting: Slice and dice financial data across multiple dimensions, entities, departments, projects, and locations.
• Workflow management: Built-in approval workflows for proper authorization and documentation of intercompany transactions while maintaining audit trails.

Best Practices for Managing Intercompany Transactions

Implementing the right software is only part of the solution. Consider these best practices.

Best Practice	How Accounting Software Helps
Establish Clear Policies	Create standardized transaction types, pricing rules, and approval workflows within the system.
Maintain Detailed Documentation	Store intercompany transactions and agreements digitally for easy access and audit compliance.
Regular Reconciliation	Automate reconciliation processes and generate discrepancy reports for quick resolution.
Automate Where Possible	Use automation features to reduce manual errors in recording, matching, and eliminating intercompany transactions.
Train Your Team	Provide training to help accounting staff understand intercompany accounting principles and software usage.

Choosing the Right Solution for Your Business

The choice between these accounting software solutions depends on several factors.

Business Size and Complexity

Sage Intacct and NetSuite software are typically better suited for larger, more complex organizations, while QuickBooks and Xero work well for smaller businesses with simpler needs. Consider your business's size and complexity.

International Operations

Companies with significant international presence should prioritize solutions with strong multi-currency and localization features.

Integration Requirements

Consider your existing technology stack and choose software that integrates well with your currency system to prevent implementation issues.

Budget Considerations

Balance the cost of implementation and ongoing licensing with the potential efficiency gains and risk reduction. While some of these accounting software programs offer advanced features, they may not fit your business’s budget.

Growth Plans

Choose a solution that can scale with your business rather than requiring replacement as you grow. For example, if you have a small to mid-sized business and are using QuickBooks, continuing with them and using their Enterprise plan may be the right choice.

Summing Up

Managing intercompany transactions effectively takes more than basic bookkeeping software for multiple businesses. The right multi-company accounting software online can transform complex financial processes into streamlined, automated workflows that save time and reduce errors.

Sage Intacct leads the pack for enterprises requiring sophisticated consolidation and reporting capabilities. NetSuite software offers the most comprehensive all-in-one solution for growing businesses. Microsoft Dynamics 365 provides powerful integration for Microsoft-centric organizations. QuickBooks Enterprise offers familiarity and affordability for smaller multi-entity operations. Xero delivers an exceptional user experience for straightforward multi-entity needs.

The key is matching your specific requirements with the right solution. Consider starting with a pilot implementation or requesting detailed demos to see that the chosen platform aligns with your business processes and growth objectives. With the right enterprise financial software in place, managing multi-entity accounting becomes a strategic advantage rather than an operational burden.

Save Time and Money On Overseas Payments With Wise Business

Wise Business can help you save big time on international payments.

Wise is not a bank, but a Money Services Business (MSB) provider and a smart alternative to banks. The Wise Business account is designed with international business in mind, and makes it easy to send, hold, and manage business funds in currencies.

Signing up to Wise Business allows access to BatchTransfer which you can use to pay up to 1000 invoices in one go. This is perfect for small businesses that are managing a global team, saving a ton of time and hassle when making payments.

Some key features of Wise Business include:

• Mid-market rate: Get the mid-market exchange rate with no hidden fees on international transfers

• Global Account: Send money to countries and hold multiple currencies, all in one place. You can also get major currency account details for a one-off fee to receive overseas payments like a local

• Access to BatchTransfer: Pay up to 1000 invoices in one click. Save time, money, and stress when you make 1000 payments in one click with BatchTransfer payments. Access to BatchTransfer is free with a Wise Business account

• Auto-conversions: Don't like the current currency exchange rate? Set your desired rate, and Wise sends the transfer the moment the rate is met

• Free invoicing tool: Generate and send professional invoices

• No minimum balance requirements or monthly fees: US-based businesses can open an account for free. Learn more about fees here

Use Wise Business >>

---

Sources:

1. NetSuite dashboards: a starter guide | NewGen Business Solutions
2. Sage Intacct | Abdo
3. Reporting and dashboards | Eventura
4. NetSuite Suite Analytics Reporting & Dashboards | Netsuite