ERP Software for Biotechnology
Biotechnology companies face a unique ERP challenge: they must manage the financial complexity of pre-revenue research organizations, the operational demands of clinical trial supply chain and investigational product manufacturing, and — upon commercial launch — the stringent FDA regulatory requirements of biologics manufacturing under 21 CFR Part 211 and the PHSA. ERP systems must scale across these radically different operational stages, supporting grant and milestone accounting in early development through fully validated GMP manufacturing ERP at commercial scale.
Compare ERP Systems for Biotechnology
Select up to 4 ERP vendors to compare side by side. Filtered to show systems with strong biotechnology capabilities.
Key Challenges for Biotechnology
Managing financial operations across multiple stages of development — preclinical, clinical, and commercial — with fundamentally different accounting, reporting, and compliance requirements at each stage
Tracking clinical trial supply chain for investigational medicinal products (IMPs) across global clinical sites with temperature-controlled distribution and chain of custody requirements
Achieving FDA and EMA approval for biologics manufacturing ERP systems requiring formal computer system validation at commercial scale
Managing complex contract manufacturing organization (CMO) relationships for drug substance and drug product manufacturing with batch records, material control, and quality oversight
Maintaining accurate grant accounting, milestone recognition, and collaborative R&D agreement (CRADA) financial tracking under US GAAP and IFRS
Controlling R&D expenditures across multiple programs, compounds, and clinical trials with project-level cost visibility and capitalization analysis
Coordinating material requirements across internal research labs, external CMOs, and clinical logistics providers with complex temperature and handling requirements
Best Biotechnology ERP for SMBs
Recommended for companies with $10M–$250M revenue and 10–200 employees.
Sage Intacct
mid-rangePreferred financial management platform for pre-revenue and growth-stage biotech companies. Strong grant management, milestone revenue recognition, multi-entity consolidation, and HIPAA-ready cloud environment.
Best for: Pre-revenue and early-commercial biotech companies with complex grant and milestone accounting
NetSuite
mid-rangeCloud ERP with strong financial management, project accounting, and inventory capabilities well-suited to clinical-stage biotech companies managing multiple compounds and cost centers.
Best for: Clinical-stage biotech companies managing multi-program financial tracking
Microsoft Dynamics 365 Business Central
mid-rangeCloud ERP with flexible financial management, project accounting, and inventory for biotech companies seeking accessible operations management during clinical development.
Best for: Series B and Series C biotech companies scaling operational infrastructure
Acumatica
mid-rangeCloud-native ERP with strong project accounting, distribution, and inventory management supporting biotech companies managing clinical supply and external manufacturing partners.
Best for: Growth-stage biotech companies with emerging supply chain complexity
HealthStream
mid-rangeLearning management and workforce development platform specialized for healthcare and life sciences organizations managing GMP training requirements, SOPs, and regulatory competency documentation.
Best for: Biotech companies building GMP training infrastructure for pre-commercial manufacturing
Intact IQ
mid-rangeModern cloud ERP with strong financial management and distribution capabilities for biotech companies managing complex supplier relationships and multi-currency procurement operations.
Best for: Biotech companies with significant procurement and distribution complexity
Best Biotechnology ERP for Enterprise
Recommended for companies with $250M+ revenue and complex multi-site operations.
SAP S/4HANA
enterpriseGlobal standard for large commercial biotech manufacturers with validated process manufacturing, batch genealogy, biologics-specific production management, and integration to leading QMS and MES platforms.
Best for: Large commercial-stage biologics manufacturers with global operations
Oracle ERP Cloud
enterpriseComprehensive cloud platform with pharmaceutical and life sciences manufacturing capabilities, clinical trial management integration, and advanced financial management for large biotech enterprises.
Best for: Large diversified biotech companies seeking integrated commercial-stage ERP
Infor CloudSuite Healthcare
enterpriseHealthcare and life sciences ERP with supply chain, quality, and financial management validated for FDA-regulated manufacturing environments. Strong fit for mid-to-large biologics manufacturers.
Best for: Commercial-stage biologics companies prioritizing healthcare industry depth
Microsoft Dynamics 365 Finance & Supply Chain Management
enterpriseEnterprise ERP with process manufacturing, lot traceability, and quality management capabilities for commercial biotech companies operating within the Microsoft ecosystem.
Best for: Large biotech companies with strong Microsoft technology investments
Essential ERP Capabilities for Biotechnology
Grant accounting and milestone revenue recognition under ASC 808 and ASC 606 for collaborative agreements
Research project cost tracking with compound-level, program-level, and cost center-level expenditure visibility
Clinical trial supply chain management with temperature-controlled distribution and IMP chain of custody
Contract manufacturing organization (CMO) management with purchase order control, batch record reconciliation, and quality hold workflows
FDA 21 CFR Part 11 and Part 211 compliant electronic records for commercial biologics manufacturing
Biologic drug substance and drug product batch management with full genealogy and deviation tracking
R&D expense capitalization analysis for project transition from development to commercial asset
Multi-entity financial consolidation for holding company, operating subsidiary, and clinical site structures
Cold chain and controlled substance inventory management with chain of custody documentation
Technology transfer documentation management for CMO and internal manufacturing site scale-up
Biotechnology ERP Cost Ranges
SMB
$50,000 – $200,000
10–60 users
Implementation: $40,000 – $175,000
Mid-Market
$200,000 – $900,000
60–250 users
Implementation: $200,000 – $1,000,000
Enterprise
$1,000,000 – $8,000,000+
250–2,000+ users
Implementation: $2,000,000 – $12,000,000+
Implementation Considerations
Select an ERP platform that can scale from pre-revenue financial management through commercial GMP manufacturing without requiring a platform replacement at launch — migration between ERP systems at the time of FDA approval is extremely high-risk
Design grant and milestone accounting workflows in collaboration with your accounting firm and investor relations team before configuration to ensure compliance with ASC 808, ASC 606, and SEC reporting requirements
Plan clinical supply chain ERP requirements with your clinical operations and CMC (chemistry, manufacturing, and controls) teams — regulatory authorities scrutinize clinical supply chain documentation at the IND and NDA/BLA stages
Budget for computer system validation at commercial stage even if operating in a non-validated environment during development — FDA inspection preparedness requires validated commercial manufacturing systems before or at BLA approval
Engage experienced life sciences ERP implementation partners who understand both the pre-commercial financial accounting complexity and the commercial GMP validation requirements of biotechnology companies
Frequently Asked Questions
What ERP do most biotech companies use before commercialization?
Pre-revenue and clinical-stage biotech companies most commonly use Sage Intacct or NetSuite for financial management due to their strong grant accounting, milestone revenue recognition, and multi-entity capabilities without enterprise implementation cost. As companies approach commercial launch, many migrate to SAP S/4HANA, Oracle ERP Cloud, or Infor CloudSuite for GMP manufacturing management, often retaining the pre-commercial financial platform in parallel during the transition.
How does grant accounting work for biotech companies in ERP?
Grant accounting in biotech ERP involves tracking government and foundation grants as restricted funding sources, applying expenditures to the correct grant cost category (direct vs. indirect), recognizing revenue based on expenditure milestones or deliverables, generating grant-specific financial reports for federal agencies (SF-425 for NIH grants), and managing grant compliance documentation. ASC 958 and ASC 808 provide the US GAAP framework for grant and collaborative agreement accounting in life sciences.
What is ASC 606 milestone revenue recognition and how does ERP support it?
ASC 606 requires biotech companies with partnership and licensing agreements to allocate transaction prices to distinct performance obligations (milestones, licenses, manufacturing services) and recognize revenue when or as each obligation is satisfied. ERP systems support ASC 606 compliance through contract management modules that define performance obligations, automate revenue allocation, trigger recognition upon milestone completion, and generate disclosure-ready deferred revenue schedules for financial statement presentation.
How do biotech companies manage CMO relationships in ERP?
Contract manufacturing organization (CMO) management in biotech ERP covers purchase order issuance for drug substance and drug product manufacturing runs, receipt of batch record and certificate of analysis documentation, quality hold and release workflows for CMO-manufactured material, invoice reconciliation against actual batch yields, and performance metrics tracking. Strong supplier quality management modules that enforce quality agreements and capture batch disposition decisions are essential for GMP compliance across CMO relationships.
What is technology transfer and how does ERP support it?
Technology transfer is the formal process of moving a manufacturing process from a development or research environment to a commercial-scale manufacturing site (internal or CMO). ERP supports technology transfer by managing the transfer of master batch records, specifications, and analytical methods as controlled documents, tracking the qualification batches manufactured at the receiving site, managing material and supply qualifications, and documenting the transfer in change control records required by FDA for BLA or NDA supplements.
When should a biotech company implement a GMP-validated ERP?
Biotech companies should begin planning GMP ERP validation no later than Phase III clinical trials, with implementation targeting completion 18–24 months before anticipated BLA or NDA submission. FDA expects that commercial manufacturing systems are validated and in use before approval, and many companies receive FDA questions about their commercial manufacturing IT infrastructure during pre-approval inspections (PAIs). Waiting until after approval creates unacceptable operational and compliance risk.
How do biotech companies track R&D expenses by compound and program in ERP?
R&D expense tracking by compound and program uses project accounting or cost center hierarchies in the ERP. Each drug program or compound is defined as a project or cost center, with sub-projects for clinical stages (Phase I, II, III) and functional areas (clinical operations, CMC, regulatory). Purchase orders, vendor invoices, and internal labor charges are coded to the appropriate program and stage, enabling program-level burn rate reporting, capitalization analysis, and investor transparency into pipeline expenditures.
What is the biggest financial risk in a biotech ERP implementation?
The highest financial risk in biotech ERP is implementing a platform that cannot scale to GMP manufacturing requirements at commercial launch, requiring a full ERP replacement during or immediately after the FDA approval process. The second major risk is ASC 606 and ASC 808 revenue recognition misconfiguration — errors in milestone revenue recognition can require restatements that are highly disruptive for public biotech companies. Engaging accounting firm advisors alongside ERP implementation partners from the start significantly reduces both risks.
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