Skip to main content
Partner Stories

Regulatory-Ready: Using Dynamics 365 Finance for Pharma & Biotech Financial Compliance (FDA, EMA)

Dynamics 365 Finance for the pharmaceutical industry can be instrumental in streamlining financial processes, tracking expenses, and maintaining compliance with industry regulations.

Finance leaders in the pharmaceutical and biotech industry face growing pressure to comply with complex regulations from agencies like the FDA (U.S. Food & Drug Administration) and EMA (European Medicines Agency). Add to this the demands of handling audits, tracking R&D credits, managing global tax rules, and ensuring complete traceability. And without the right systems in place, managing compliance can become quite overwhelming.

This is where Microsoft Dynamics 365 Finance steps in. Tailored for industries that rely heavily on compliance and reporting, Dynamics 365 Finance for the pharmaceutical industry provides the control, transparency, and automation needed to stay audit-ready, reduce risk, and maintain financial accuracy across the board.

Why Compliance Matters in Pharma & Biotech

In the pharmaceutical and biotech space, financial compliance is not just about staying out of trouble but also about product approval, investment, and business continuity. Regulatory bodies expect strict adherence to accounting standards, transparent documentation, and accurate financial reports that trace back to every transaction.

For example:

  • The FDA demands clear cost tracking for clinical trials.
  • The EMA requires financial transparency for companies operating across EU countries.
  • Inaccurate handling of R&D tax credits can result in hefty penalties or missed benefits.

This is why using an advanced ERP for pharmaceutical financial compliance isn’t optional but a useful tool.

Dynamics 365 Finance for Pharmaceutical Industry

Dynamics 365 Finance for pharmaceutical industry is designed to handle complex financial operations. It supports pharmaceutical businesses in the following ways:

1. End-to-End Financial Visibility

Using Dynamics 365 Finance for pharmaceutical industry, you can track every transaction, grant, and expense across departments and global subsidiaries. Financial records are automatically updated and available in real time, helping teams monitor trial costs, production expenses, and global tax requirements in one place.

2. Audit-Ready Document Management

Dynamics 365 Finance for pharmaceutical industry keeps a complete audit trail of every financial action. Whether it's a journal entry or a tax adjustment, records are easy to access and review, making regulatory audits less stressful and more efficient.

3. Global Compliance Features

Pharma companies working across borders benefit from built-in localisation and compliance support. Dynamics 365 Finance supports country-specific tax rules, financial standards, and regulatory formats needed for FDA compliance, financial ERP and EMA compliance financial system reporting.

4. Cost Control and Budgeting

With built-in budgeting and forecasting tools, finance leaders can plan and adjust costs throughout drug development stages. You can allocate resources accurately to departments like manufacturing, QA, and regulatory affairs.

Dynamics 365 Finance for Biotech Industry

For biotech companies, often startups or scale-ups, speed and accuracy matter just as much as compliance. Here, Dynamics 365 Finance for the biotech industry offers various benefits, including:

Key Benefits:

  • Project-based tracking: With Dynamics 365 Finance for biotech, companies involved in R&D can link expenses to specific trials or phases.
  • Grant and funding management: Dynamics 365 Finance for biotech makes it easier to handle public and private research funding and track it by source.
  • Investor reporting: Using Dynamics 365 Finance for biotech, generate clean, real-time reports for stakeholders and investors without needing to pull data manually. 

This makes Dynamics 365 for biotech companies not just a financial tool but a biotech financial management system that supports innovation, transparency, and compliance.

How Dynamics 365 Helps with R&D Tax Credit Handling

R&D tax credits are a key benefit in pharma and biotech, but only if tracked and reported correctly.

With Dynamics 365 Finance, you can:

  • Tag and track eligible R&D expenses across projects and teams. 
  • Generate reports for specific tax jurisdictions.
  • Maintain supporting documentation for audits.

This ensures businesses don’t miss out on R&D tax incentives while keeping their records clean for regulators.

Financial Compliance in Pharmaceutical Manufacturing

Manufacturing in the pharma industry demands full traceability, not just for products but also for finances. Here, Dynamics 365 supports:

  • Batch costing: Assign costs directly to production batches.
  • Resource tracking: Monitor time, equipment, and labour linked to production.
  • Lot-level accounting: Ensure costs can be traced to specific production lots, supporting validation processes.

This meets compliance demands while keeping operations efficient and finance teams informed.

Integration with Other Microsoft Tools

Dynamics 365 Finance is built to work with:

  • Microsoft Power BI for advanced analytics
  • Dynamics 365 Supply Chain Management for inventory and distribution
  • Microsoft Teams and Outlook for smoother collaboration and communication
     

All of these tools enhance visibility and support faster decision-making across departments.

Real-World Example

A mid-sized pharmaceutical company using Dynamics 365 Finance saw the following results within the first year:

  • Reduced audit preparation time by 50%
    Automated tools in Dynamics 365 Finance help finance teams gather records faster and keep everything organised. This makes it easier to get ready for audits with less effort.
  • Saved 30% in manual reporting costs
    By reducing the need for manual work and external reporting services, companies have been able to cut costs and improve reporting speed.
  • Increased R&D tax credit claims accuracy
    With better tracking of R&D spending and built-in audit trails, businesses can report qualifying expenses more accurately and reduce the risk of missing out on credits.

With one integrated platform, they connected financial data from labs, production lines, and clinical trials, ensuring better control and audit readiness.

Why Choose Dynamics 365 Finance for Pharmaceutical and Biotech?

Choosing Dynamics 365 Finance for pharmaceutical and biotech companies has multiple benefits, where some of its key benefits include:

Real-time data access
Finance teams can view updated figures across departments instantly. This helps avoid delays in reporting, budget reviews, and audit prep.

Regulatory reporting compliance
Built-in features support FDA, EMA, and other regional standards. Reports can be generated in formats accepted by regulatory bodies, reducing the risk of errors.

Supports multi-entity operations
Easily manage the financials of global branches, subsidiaries, or research sites, all within a single platform. Currency and tax differences are handled automatically.

Simplifies global tax and audit processes
Stay compliant with country-specific tax laws and maintain a full audit trail. This reduces manual tracking and speeds up audit responses.

Works well with biotech funding models
Whether you’re managing grants, private equity, or public funding, Dynamics 365 keeps the records clean and linked to the right projects or phases.


Whether you're a well-established global pharma company or a growing biotech startup, Dynamics 365 is designed to scale as your business grows.

Final Thoughts

If you are doing business in an industry where compliance isn't optional, your ERP system should do more than basic accounting. Dynamics 365 Finance for pharmaceutical industry brings control, automation, and audit readiness into one platform.

Dynamics 365 Finance for pharmaceutical industry system is worth investing in if you're looking to simplify compliance with the FDA, EMA, and other regulatory bodies while improving your financial accuracy and reporting.

Let’s talk!

If you're exploring ERP solutions for your pharma or biotech business, we’re here to help.

Contact Dynamics Square today and find out how to implement Dynamics 365 Finance for pharmaceutical and biotech industries and enable support for your compliance needs and financial goals.