As biotech companies scale, user-friendly software systems—like EQMS, LIMS, or MES— can help standardize operations, ensure data integrity, and support regulatory compliance. But before signing a contract, it’s critical to better understand what the system can do and how it’s built, maintained, and supported behind the scenes.

So, how do you dive into what really matters? It starts with asking the right questions—ones that reveal how the vendor approaches compliance, data integrity, security, and customer support. Here are the key areas to focus on and examples of the questions you should be asking.

Start with Regulatory Compliance and Validation Readiness

You need to know if the software provider understands the regulatory space you operate in. Ask vendors if their system supports compliance with standards like 21 CFR Part 11, Annex 11, and GAMP 5. You might say, “Can you share your validation documentation, such as Installation Qualification (IQ) or Operational Qualification (OQ) reports?” or “How does your system ensure data integrity and handle electronic signatures?”

Explore Their Development and Change Management Process

A mature Software Development Lifecycle (SDLC) and structured change control are key to long-term stability. You might ask, “How do you manage updates and hotfixes, and how are changes tested before they’re pushed to production?”

Ask whether they follow Agile, Waterfall, or hybrid methodologies, and how they document development decisions. Discuss if they have a version control system, documented regression testing, and can walk you through their process for handling critical patches.

Understand Data Hosting, Security, and Backup Protocols

For cloud-based systems, data residency and security are hot-button topics. Vendors should be able to confidently answer, “Where is our data stored, and what certifications do your data centers hold?” and “What measures are in place for disaster recovery and business continuity?”

If it’s a multi-tenant system, ask, “How is our data isolated from other clients’ data?” You’ll want to verify that encryption is used both in transit and at rest and that access is limited through robust identity and access management (IAM) controls.

Ask About Access Controls and User Management

Any GxP-compliant system needs to have granular control over user roles and permissions. A helpful question might be, “Can roles be configured to enforce segregation of duties, and can permissions be tied to organizational hierarchy?”

Additionally, ask whether the system supports single sign-on (SSO) or Active Directory integration—especially if you’re looking to scale or maintain centralized control across multiple systems.

Don’t Skip Customer Support and Issue Handling

While everyone talks about features, few talk about how support issues are handled in real time. Ask, “What is your average response time for critical tickets?” or “Do you offer 24/7 support for system outages?”

Some vendors offer tiered support, while others may assign a dedicated customer success manager. Be sure to ask for real-world support metrics—response times, resolution times, and even customer satisfaction scores.

Check for Biotech-Specific Experience

It’s important that your software partner understands your domain. Ask, “Do you have experience working with biotech or pharmaceutical companies, and can you share references?” You can also dive deeper with questions like, “How do you support deviations, CAPAs, or batch record review?”

A vendor who understands the difference between a QA-led process and an R&D workflow is more likely to build a system that aligns with your needs.

Discuss Configurability Without Over-Customization

You want a system that fits your workflows without breaking every time an upgrade happens. Good questions include, “What parts of the system can be configured without custom code?” and “How do you track changes to configurations, and are they included in audit trails?”

This is especially important for scaling biotech companies that are still refining their processes. Flexibility is great—but only if it doesn’t compromise control or validation status.

Talk About Integration and Migration Support

If you’re moving off spreadsheets or an outdated system, you’ll need to understand the migration path. Ask vendors, “Can you support data migration from our existing systems?” and “What’s your approach to ensuring data integrity during migration?”

Also, explore API capabilities or built-in connectors if you’re expecting the system to talk to ERP systems, PAS-X, or other platforms in your tech stack.

Look Into Their Product Roadmap and Upgrade Policy

Understanding a vendor’s future plans can help you assess whether their vision aligns with your company’s growth. Ask, “Do you publish a product roadmap?”

Also clarify whether upgrades are optional or mandatory, and how they’re managed for validated environments.

Clarify the Fine Print on Pricing and Licensing

Finally, don’t forget to dig into the contract details. Ask, “What’s included in the base license, and what’s considered an add-on?” or “Are there any hidden costs for additional environments, support, or integrations?”

Understanding the exit strategy is just as important—ask, “How is our data returned to us if we terminate the agreement?”

Selecting the right software vendor goes far beyond features and functionality. For biotech companies operating in highly regulated environments, it’s about ensuring that your partner understands your industry, supports compliance, and can scale with your business.

By asking thoughtful, specific questions during a vendor audit, you empower your team to make a decision that safeguards your operations today and supports your vision for tomorrow.