Pharma & Biotech ERP: GxP compliance, batch traceability and serialization
A pharmaceutical ERP must meet requirements that few industries face: good manufacturing practices, batch and serial number traceability, computerized system validation and data integrity. With Microsoft Dynamics 365 Finance & Operations, FiveForty helps laboratories, pharmaceutical manufacturers, biotechs and contract manufacturers secure their operations.

What is a pharmaceutical ERP?
A pharmaceutical ERP is an integrated management software package able to manage production, quality, inventory, purchasing and finance for a company subject to a strict regulatory framework. What sets it apart is not functional but evidential: every operation must be recorded, time-stamped, attributable to an identified user and reconstructable years later.
ERP, LIMS and MES: who does what?
The LIMS manages the laboratory: samples, analyses, results. The MES runs the shop floor: real-time production orders, machine parameters, electronic batch record. TheERP orchestrates the company: planning, procurement, inventory, costs and accounting. The three are complementary and must communicate: an analysis result must be able to release a lot in the ERP without re-entry.
Why a generic ERP is not enough
A standard ERP knows how to manage inventory. It cannot natively block a batch in quarantine until quality control has ruled on it, trace a serial number all the way to the patient, or produce an audit trail that meets an inspector’s expectations. These capabilities depend on the configuration and industry expertise of the integrator far more than on the choice of software vendor.
ERP for the pharmaceutical industry
Drug manufacturing requires a level of document control that no other industrial sector demands.
Batch records and good manufacturing practices
The GMP (good manufacturing practices, or GMP internationally) require that every lot produced be documented end to end: raw materials used, equipment, parameters, operators and checks performed. The ERP must build this record automatically, not reconstruct it after the fact.
Batch management, quarantine and release
A manufactured batch is not a sellable batch. It remains in quarantine status until the release decision, which is made based on test results. The ERP must manage these statuses, physically and logically block unreleased inventory, and keep a record of who released what and on what basis.
Quality control and non-conformities
Inspection plans, sampling, deviations, CAPA (corrective and preventive actions), change control. These quality processes must live in the same system as production; otherwise discrepancies are resolved by email and disappear from the records.
Cold chain and controlled storage
Temperatures, dedicated storage zones, products under special status: location management must reflect actual physical constraints. An untracked break in the cold chain becomes both a product risk and a regulatory risk.
Batch recall and pharmacovigilance
In the event of a recall, the question is simple: where did this lot go, and how quickly can you locate it? A properly configured ERP reconstructs the complete genealogy (incoming materials, lots produced, customers shipped to) in a matter of minutes.
Contract manufacturers, CDMOs and subcontracting
Many companies entrust all or part of their production to contract manufacturers. The ERP must manage subcontracting: supplying materials, tracking work in progress at the third party, receiving and inspecting the finished product, with the same traceability as in-house.
“ In pharma, what is not recorded did not happen.”
Biotech ERP: very distinct needs
A biotech is not a small pharma company. Its model, its pace and its funding constraints change everything.
From research to production: scaling up
A biotech moves from the lab to pilot scale and then to industrialization, sometimes within a few months. The ERP must support this scale-up without having to rebuild everything at each stage: the structure of bills of materials and routings must evolve, not be redone.
Clinical trials and clinical batch management
Batches intended for trials follow their own rules: randomization, blinded labeling, traceability by investigator site, product accountability. These flows are unlike any standard commercial flow.
Tracking of R&D costs and funding
Grants, research tax credit, fundraising, partnerships: a biotech must justify how its spending is allocated by program and by funding source. Project-based cost accounting becomes a survival tool, not a convenience.
Rapid growth and headcount doubling
Growing from twenty to two hundred people in two years puts every process to the test. A structuring ERP enforces approval workflows from the start and avoids the organizational debt that has to be paid later at audit time.
Intellectual property and confidentiality
Formulas, processes, results: the company’s most sensitive data passes through the system. Fine-grained rights management, project-level segregation and access logging are not optional.
Partnerships and the CDMO model
Many biotechs do not manufacture themselves and work with CDMOs. The ERP must manage this relationship: process transfer, tracking of batches produced by the partner, quality control on receipt.
Regulatory compliance and validation
In a regulated environment, the ERP itself is subject to compliance, not just a tool.
GxP: GMP, GLP and GCP
Master data GxP cover manufacturing (GMP), laboratories (GLP) and clinical trials (GCP). They require written procedures, complete records and proof that the system does what it is supposed to do.
FDA 21 CFR Part 11 and European Annex 11
These texts govern electronic records and signatures: unique user identification, attributable signatures, an unalterable audit trail, version management. The 21 CFR Part 11 applies as soon as you export to the United States; the Annex 11 of the EU GMP covers computerized systems in Europe.
Computerized system validation (CSV)
An ERP in a GxP environment must be qualified: installation, operational and performance qualification (IQ, OQ, PQ), with validation documentation maintained at every version upgrade. It is a workstream in its own right, to be planned from the scoping phase.
Data integrity and the ALCOA+ principle
Data must be attributable, legible, contemporaneous, original and accurate, as defined by ALCOA+. In practice: no change without a trace, no deletion, no unjustified retroactive entry.
Preparing for inspections
ANSM, EMA, FDA: an inspection largely consists of requesting evidence. A system that produces this evidence in a few clicks turns an ordeal into a formality and greatly reduces the internal cost of compliance.
Our Dynamics 365 solutions for Pharma and Biotech

End-to-end serialization and traceability
The fight against falsified medicines has made unique identification of each pack mandatory. It is now one of the most structural workstreams in the industry.
Serialization and the Falsified Medicines Directive
Each pack carries a unique identifier, registered in a European repository and verified at dispensing. The ERP must generate, assign and transmit these numbers, then handle special cases: reprinting, destruction, returns.
Upstream and downstream traceability
Tracing back from a finished product to its raw materials, and forward from a raw material to every lot that contains it: this two-way genealogy is the first thing an inspector asks for.
Unique device identification (UDI) for medical devices
Medical device manufacturers fall under the European MDR regulation and the obligation ofUDI. The logic is similar to pharmaceutical serialization and relies on the same foundations in the ERP.
Integration with LIMS and MES
Test results must automatically trigger the release or blocking of a batch in the ERP; shop floor data must feed the batch record. Without these interfaces, traceability remains manual, and therefore fragile.
Serialization for export
Each market has its own rules: the European approach, American requirements, Asian frameworks. An exporting company must be able to manage several serialization schemes in a single system.
Assigning roles properly
The first mistake in a project in a regulated environment is asking one tool to do what another does better.
ERP, LIMS or MES: the comparison
| Criterion | LIMS | MES | ERP |
|---|---|---|---|
| Domain | The laboratory | The workshop | The company |
| Manages | Samples and analyses | Production orders | Inventory, purchasing, finance |
| Time | By test | Real time | Planning |
| Traceability | Results | Batch record | Complete genealogy |
| Lot release | Provides the result | Records execution | Changes the inventory status |
All three must be interfaced: the quality of the exchanges, more than the choice of each component, determines how robust traceability is.
Why Dynamics 365 for pharma and biotech
FiveForty is a Microsoft Dynamics 365 Finance & Operations integrator and partner.
Native batch and serial number management
Lot and serial tracking dimensions, expiration dates, inventory statuses, upstream and downstream genealogy: these mechanisms are standard and require no custom development.
Integrated quality and inspection
Quality control plans, quality orders, automatic blocking of nonconforming inventory and nonconformance management are part of the Supply Chain Management core.
Audit trail and security
Change logging, granular role management and segregation of duties provide the foundations expected by GxP frameworks, to be documented afterwards in your validation file.
Multi-site, multi-country and consolidation
Multiple legal entities, multiple currencies, multiple regulatory frameworks in a single instance: an asset for growing groups or those expanding internationally.
Management with Power BI
Yield indicators, non-conformance rates, release lead times, costs per lot: dashboards fed directly by the ERP, with no intermediate export.
Our support, from scoping to application maintenance
Regulatory scoping, configuration, data migration, validation support, training, then application maintenance to absorb version upgrades without breaking compliance.
The benefits of an ERP for pharma and biotech
- Full traceability of batches, serial numbers and operations, both upstream and downstream
- Lot recall reconstructed in minutes rather than days
- Serialization managed natively, including for export
- Tool-supported GxP compliance : audit trail, signatures, data integrity
- Inspections prepared : evidence is produced in a few clicks
- Built-in quality : quarantine, release and CAPA in the same system
- Controlled costs by lot, by project and by funding source
- Growth absorbed : from pilot to industrialization without starting over
- Managed subcontracting with the same rigor as in-house
A question? An answer.
Frequently asked questions
A pharmaceutical ERP is an integrated management software package designed to manage production, quality, inventory and finance for a company subject to good manufacturing practices. It stands out for its ability to trace every batch, manage release statuses and produce an audit trail that complies with regulatory requirements.
A biotech needs an ERP that can support its scale-up, track its R&D costs by program and by funding source, and manage subcontracting with CDMOs. Microsoft Dynamics 365 Finance & Operations meets these needs thanks to its modularity and project-based cost accounting.
The LIMS manages the laboratory (samples, tests, results), the MES runs the shop floor in real time along with the batch record, and the ERP orchestrates the company (planning, inventory, purchasing, costs, accounting). The three are complementary and must be interfaced to avoid re-entering data.
An ERP is not compliant in itself: its configuration, validation and associated procedures are what make it compliant. Dynamics 365 provides the necessary foundations (user identification, audit trail, rights management), which must then be documented in a validation file.
The ERP generates and assigns unique identifiers to the units produced, sends them to the regulatory repositories and manages lifecycle events: reprinting, destruction, return, export. It keeps the link between each serial number, its batch and its destination.
A rollout in a GxP environment takes longer than a standard project because it includes the validation of computerized systems. Allow several months depending on the scope, the number of sites and the required level of qualification. A scope focused on finance and supply chain can start more quickly.
Yes. Dynamics 365 is suited to a biotech of a few dozen people as well as a multi-site pharmaceutical group, thanks to a modular approach that lets you start with a limited scope and then expand as you grow.
Yes. Power BI integrates natively with Dynamics 365 and makes it possible to produce dashboards on yields, non-conformance rates, release lead times and costs per batch, directly from ERP data.


