FAT/SAT pharma: a practical guide to hitting GMP milestones in Switzerland

Commissioning a new pharmaceutical line in Switzerland goes through two critical milestones: the Factory Acceptance Test (FAT) at the OEM site, and the Site Acceptance Test (SAT) at the client site. Poorly prepared, these two moments cause projects to slip by months and cost dearly in penalties, time-to-market delays and team stress. Well prepared, they are an opportunity to stabilize a line before it touches production.

This article gathers what we have learned over more than 10 years of pharma automation commissioning on sites such as Merck Serono in Corsier-sur-Vevey, Takeda fill & finish, Lonza and several Basel-based players. It is intended for project managers, validation engineers, site leads and automation engineers who are preparing or facing a FAT/SAT in a GMP environment.

The FAT / SAT difference, and why it matters

Factory Acceptance Test (FAT). Test performed at the OEM site before equipment shipment. The client (the pharma manufacturer) travels to the supplier to verify the machine matches functional and technical specifications (URS, FDS, HDS). It's the last point where you can request major changes without massive cost overruns.

Site Acceptance Test (SAT). Test performed on the final site after installation, utility connection (water, steam, air, electricity, OT network) and integration with adjacent systems (SCADA, MES, quality). The SAT verifies the machine works in its real environment.

These two steps then feed the Installation Qualification (IQ), Operational Qualification (OQ) and Performance Qualification (PQ) that make up the GMP validation dossier.

The sequence is therefore: URS → FDS → HDS → FAT → shipment → SAT → IQ → OQ → PQ → routine.

The three success plans for a FAT

1. Prepare the documentation upstream, not during

On FATs that slip, the number-one cause we see is almost always the same: documentation arrives at the same time as the test, or after. FAT protocols, checklists, test data sets, objective evidence to collect — all of this must be written, reviewed and approved by quality before the test starts.

Concretely:

The FAT protocol covers all URS and FDS requirements with line-by-line traceability.
Test data sets cover nominal AND degraded cases (alarms, interrupted batch, restart, sensor failure).
Checklists specify who signs what, with what evidence (screenshot, instrument measurement, machine report).

If you arrive at the supplier without these validated documents, you will improvise. And improvising in pharma means rejecting the FAT internally or reopening deviations later in GMP.

2. Anticipate deviations

In 100% of the FATs we have supervised, there are deviations. It's normal. The question is not "will there be deviations" but "how do we manage them".

Best practice: have a pre-printed deviation register (or more modern, in a tool like Kneat or Veeva Vault) with columns: number, description, criticality (minor / major / critical), required action, owner, due date. Each deviation must be addressed before the SAT — otherwise it cascades back later.

FAT-blocker criteria (must be resolved before shipment):

Any functional safety deviation (SIL, ESD, PPE).
Any deviation impacting GMP compliance (data integrity, audit trail, user access).
Any deviation on critical business functions (batch recipe, material traceability, serialization).

Minor deviations (cosmetic HMI, labels, slight adjustments) can be addressed at SAT without blocking shipment.

3. Delegate to an automation engineer who has done this before

The FAT is a moment where coordination between the OEM automation team, the client automation team, validation, quality and process engineering must be fluid. If your internal team has never run a FAT, you will lose time learning on the spot.

This is typically where subcontracting to a senior automation engineer experienced in similar pharma FATs makes a difference. Not to replace your team — to guide them, take technical responsibility for the test and arbitrate schedule / quality / cost trade-offs in real time.

> At [Vanguard Systems](/), we regularly take on the client-side automation project lead role on European pharma FATs. Our [project reinforcement and design office](/services) approach covers exactly this need.

The three success plans for a SAT

1. Verify the site prerequisites list

The SAT often fails for reasons that have nothing to do with the machine: utilities not connected, OT network misconfigured, missing SSL certificates, user accounts not created, central SCADA access not opened, MES integration not tested.

SAT prerequisites checklist to validate 2 weeks before the supplier arrives on site:

Process utilities (process water, WFI, pure steam, ISO-class compressed air) connected and qualified.
Energy utilities (electricity, low/high voltage, fibre optics) pulled and tested.
OT network segmented per IEC 62443, VLANs created, ACLs in place.
Active Directory accounts created with roles/permissions per site policy.
Server certificates issued (for secure OPC UA, web HMI, etc.).
Central SCADA and MES access validated read/write on relevant tags.
Change control procedures known to the supplier (otherwise they intervene non-compliantly).

If any of these prerequisites are not in place the day the supplier arrives, you pay for mobilization for nothing. And the schedule slips.

2. Test in real production conditions, not ideal ones

The classic pitfall: testing with one experienced operator, no load, optimal parameters. Everything works perfectly. Then routine starts, and you discover the line is not robust to an operator who makes a mistake, a raw material that drifts a bit, a load peak at month-end.

Well-run SATs include:

Tests with production operators (not just engineers).
Tests with real raw materials (not placebos).
Tests across multiple shifts (morning, afternoon, night).
Tests over multiple days to capture drift and slow failure modes.
Tests of degraded modes (sensor failure, communication loss, restart after outage).

It takes longer, but it reveals the real problems before the line enters GMP production. Once in routine, every incident is a deviation to document and analyse — better do it at SAT where it's still "normal".

3. Prepare the handover to operational teams

The SAT is not just a technical test, it's also when your production, maintenance and quality teams take ownership of the line. If the handover is poorly done, you will see the supplier coming back every 15 days for questions that could have been handled in initial training.

Automation handover deliverables include:

User documentation: operator guide, maintenance guide, restart procedures.
Incident runbooks: what to do if a sensor fails, if a communication is lost, if a batch is rejected.
PLC/SCADA source code versioned in your repository (Versiondog, Git, or other depending on your standard) with read access for your teams.
Up-to-date OT network diagrams with IP addresses, passwords (in vault), remote access.
OEM contact list for post-delivery support needs.
Initial training for operators and technicians, ideally in two sessions 2-3 weeks apart.

Switzerland-specific pitfalls

On Swiss pharma sites, two particularities deserve attention.

First particularity: the dual GAMP5 + Swissmedic requirement. Depending on the target market (EU, US, Switzerland, others), your validation dossier must satisfy different authorities. Many Swiss sites produce for several markets simultaneously, so the FAT/SAT must produce documentation acceptable by multiple frameworks: Swissmedic for the Swiss market, EMA for EU, FDA for US.

In practice this means: systematic 21 CFR Part 11 audit trail, GAMP5-versioned documentation, irreproachable traceability of decisions and deviations. A bit more work, but that's what prevents an FDA inspection from blocking US export from a Swiss site.

Second particularity: coordination with corporate based abroad. Many pharma sites in French-speaking Switzerland depend on a parent company based in Germany, the US or Asia. IT security policies, architecture standards, validation tools (Kneat, Veeva, Trackwise) are defined by corporate.

You must therefore align FAT/SAT with corporate standards from the URS phase. Otherwise you discover late that a tool is not approved, a network architecture is not compliant, a naming convention does not pass. And then back to spec.

How much time to plan for?

Based on our Swiss pharma experience:

FAT: 1 to 2 weeks at supplier site for a medium-complexity machine, 3 to 4 weeks for a complete fill & finish or serialized packaging line.
SAT: 2 to 4 weeks on client site, half for prerequisites and integration, half for functional tests.
IQ + OQ: 3 to 6 weeks after SAT, in parallel with final adjustments.
PQ: 4 to 8 weeks in real production conditions with validation batches.

That is a total of 3 to 6 months between machine arrival and GMP routine, depending on complexity. Any faster promise should be challenged — except for simple machines and a site already experienced with this type of equipment.

Conclusion

FAT and SAT are not formalities. They define the real quality of commissioning and condition all the rest: qualification, validation, routine entry, audits. A well-prepared FAT/SAT saves months downstream. An improvised FAT/SAT loses quarters.

Three principles to remember:

1. Prepare documentation upstream, not during the test. 2. Test in real conditions, not ideal ones. 3. Delegate technical coordination to someone who has already led this type of project in a pharma environment.

> Vanguard Systems regularly works as a FAT/SAT partner for pharma integrators and manufacturers in French-speaking Switzerland and the Basel region. To discuss an ongoing project, [contact us](/contact). To see examples of commissioning projects delivered, see our [references](/references) and our [pharma sector page](/secteurs/pharma).