Machine Qualification Runs

This topic is part of the SG Systems Global equipment, process validation & regulatory readiness glossary.

Updated December 2025 • Installation/Operational/Performance Qualification, Golden Runs, Validation Batches, IQ/OQ/PQ, Process Validation, OEE, MES, QMS • Pharma, Medical Devices, Plastics, Food, CPG, Automotive

Machine qualification runs are structured production or test runs used to demonstrate that a machine, line or cell can operate within specified limits and consistently meet quality requirements before it is released for routine use. They sit at the sharp end of equipment qualification (IQ/OQ/PQ), process validation and technical transfer: real material, real recipes, real operators, under controlled and documented conditions. Where design documents and FAT/SAT prove that equipment can work, machine qualification runs prove that it does work in your plant, on your products, with your people and controls.

“If your only proof a line is ‘qualified’ is that it ran once without alarms, you don’t have qualification—you have a successful trial. Qualification runs are the difference.”

1) What Are Machine Qualification Runs?

Machine qualification runs are the structured, often multi-lot or multi-batch runs used to demonstrate that a machine or line performs as intended under defined operating ranges. In practice, they:

• Use agreed recipes, speeds, loads and environmental conditions.
• Run long enough to expose realistic operating behaviour, not just a short demo.
• Include pre-defined sampling and inspection plans for critical quality attributes (CQAs).
• Generate documented evidence for qualification and validation reports.

They may be called “OQ runs”, “PQ batches”, “validation lots” or “golden runs”, depending on the site’s vocabulary. The common thread is that these runs are deliberately planned, controlled and documented as evidence—not just as an opportunistic attempt to “see if the line works”.

2) Why Machine Qualification Runs Matter

Skimping on machine qualification runs produces predictable problems:

• Lines that pass FAT/SAT but struggle in real production because recipes, materials or operators differ.
• Regulatory findings where process validation files do not match how equipment is actually used.
• Chronic performance issues (scrap, downtime) that were never surfaced during commissioning.
• Weak defence during complaints or recalls because there is no credible baseline of “proven acceptable” performance.

For regulated sectors, qualification runs are a core element of process validation and change control. For non-regulated sectors, they are simply good engineering practice: a chance to prove capability, tune setpoints and establish realistic performance expectations before the line is exposed to high-volume or high-risk work.

3) Relationship to IQ/OQ/PQ & Validation Batches

Machine qualification runs usually sit in the OQ/PQ and validation space:

• IQ (Installation Qualification) confirms that equipment is installed correctly with the right services and documentation.
• OQ (Operational Qualification) tests operation across defined ranges, often using challenge tests and dummy or real product.
• PQ (Performance Qualification) demonstrates that the process performs consistently under routine, long-run conditions on real product.

Machine qualification runs often correspond to OQ/PQ steps: they are the actual runs and batches where IQ/OQ/PQ protocols are executed. In many industries, a set of consecutive, successful PQ batches is required before a process is declared validated or a line is released for commercial production. Skipping or downgrading these runs leaves a hole in the validation story that is hard to patch later with spreadsheets and anecdotes.

4) Defining Acceptance Criteria & Operating Ranges

Qualification runs are only meaningful if success and failure are defined up front. Typical acceptance criteria cover:

• Product CQAs (dimensions, potency, torque, seal integrity, visual appearance, etc.).
• Process parameters within defined ranges (temperatures, pressures, speeds, cycle times).
• Throughput, yield and OEE targets appropriate for the product and equipment.
• Alarm limits, interlocks and fail-safe behaviours working as designed.

These criteria are typically derived from risk assessments, design of experiments (DoE), technical transfer packages and historical performance of similar lines. They should be explicit in the qualification protocol, not negotiated after the run. If a line consistently needs “temporary” spec waivers just to pass qualification, either the design assumptions or the acceptance criteria are wrong—and both need review before sign-off.

5) Sampling Plans, Inspection & Data Capture

Machine qualification runs generate a large volume of data. To be useful, that data must be:

• Planned via sampling plans linked to risk and regulatory expectations.
• Captured with traceability to time, position on the line, lot and equipment state.
• Consistent with production-relevant methods (not special “lab-only” tests that cannot be sustained later).
• Recorded in a form that can be reused in BMR, DHR and validation reports.

In practice, this means aligning qualification sampling with future in-process controls and release tests where possible. It also means making sure that SPC, capability analysis and trending can be done without re-keying paper into spreadsheets weeks after the event. Digital capture via MES and LIMS is highly desirable, especially for multi-site programmes.

6) Process Capability, SPC & “Golden Run” Profiles

Qualification runs often serve as the basis for capability and control decisions:

• Calculating Cp, Cpk and Ppk for key dimensions or CQAs.
• Establishing baseline control charts and expected variation patterns.
• Defining “golden run” parameter profiles that future batches should resemble.

Good qualification runs deliberately cover the intended operating window, not just a single, ideal setpoint. This gives a realistic view of how sensitive the process is and how tight control limits need to be. Poorly designed runs that only test a single condition may show impressive capability numbers that evaporate the moment real-world variation hits the line.

7) Change Control, Requalification & Lifecycle

Machine qualification is not a one-time event. Over the lifecycle of a line, changes may trigger partial or full requalification runs, including:

• Major equipment changes (drives, controls, forming tools, dosing systems).
• Significant recipe or material changes (new resin grades, excipients, packaging formats).
• Software upgrades affecting control logic, alarms or user interfaces.
• Relocation of equipment or integration into new upstream/downstream flows.

Change control processes should clearly define which changes demand new machine qualification runs, which can be covered by targeted challenge tests, and which require only documentation updates. Regulators and mature customers look for evidence that lifecycle qualification decisions are risk-based, not driven by calendar anniversaries or convenience.

8) Roles & Responsibilities – Engineering, QA, Operations & Validation

Successful machine qualification runs require clear ownership across functions:

• Engineering: Owns equipment design intent, setpoint strategy, parameter ranges and technical transfer.
• Operations: Provide realistic input on staffing, changeovers and run conditions, and execute runs per protocol.
• Quality / validation: Own qualification protocols, acceptance criteria, data review and final approval.
• Maintenance: Ensure the asset is in a suitable state for qualification and capture baseline performance for future reference.

When qualification runs are treated as “an engineering job” without QA or operations buy-in, results often fail real-world scrutiny. Shared planning and review keeps expectations realistic and ensures that the qualified state reflects how the line will actually be run day to day, not just how it was run the week the vendor was on site.

9) Digital Records, Data Integrity & Evidence

Machine qualification runs feed directly into the documentary backbone of regulated manufacturing. To stand up in audits, evidence should be:

• Captured contemporaneously in controlled systems (MES, LIMS, historians, validated spreadsheets where necessary).
• Traceable to specific runs, batches, operators, equipment and software versions.
• Protected by data integrity controls (ALCOA, audit trails, e-signatures).
• Consolidated into clearly structured reports that link protocols, raw data, analysis and conclusions.

Ad hoc paper notes, post-hoc reconstructions and unversioned share-drive files weaken the credibility of qualification runs. Digital-by-design execution and reporting—aligned with QMS expectations—is increasingly viewed as the minimum standard for equipment that materially affects product quality or patient safety.

10) Linking Qualification Runs to BMR, DHR & Release

Machine qualification runs often produce product that will be:

• Released as commercial product (if protocols allow) and included in normal BMR / eBMR flows.
• Used internally as stability, reference or comparison stock.
• Rejected or segregated if acceptance criteria are not fully met.

In any of these cases, qualification runs should be clearly identifiable in batch and device records. Release decisions need to consider both the product-level QC results and the protocol-level conclusions about machine performance. When qualification runs produce borderline or failed outcomes, the fate of the associated product must be explicitly recorded; “we think we scrapped that” is not an acceptable position during inspections or customer audits.

11) Typical Weaknesses & How to Fix Them

Common problems in machine qualification runs include:

• Protocols written at a generic level that do not reflect the actual product or equipment in use.
• Acceptance criteria defined so loosely that almost any outcome can be argued as “pass”.
• Runs executed under “special care” conditions (extra staff, extra cleaning) that will not exist in routine production.
• Data captured on paper or in local spreadsheets with poor traceability and limited analysis.
• No systematic link between qualification conclusions and ongoing monitoring (SPC, alarms, OEE trends).

Fixing these issues typically involves tightening the connection between risk assessments, protocol design, MES/QMS configuration and real-world operating conditions. Qualification runs should be uncomfortable enough to reveal weaknesses—but still representative enough that their conclusions apply to day-to-day operations, not just to a one-off showcase week.

12) Machine Qualification Runs, OEE & Capacity Planning

Although machine qualification runs are primarily about quality and compliance, they also provide valuable operational insight:

• Realistic cycle times, changeover durations and ramp-up profiles.
• Baseline scrap, rework and micro-stop patterns for OEE.
• Clarity on which products and formats are “easy” or “hard” for the line.

Using qualification runs to capture this data means capacity models and business cases are grounded in observed behaviour, not vendor brochures or optimistic estimates. It also means that when real OEE falls short of expectations months later, there is a clear reference point to investigate whether the gap is due to process drift, product mix, maintenance or organisational factors rather than inherent equipment limitations.

13) Digitalisation & Industry 4.0 – Smart Qualification

In an Industry 4.0 context, machine qualification runs can take advantage of:

• High-frequency data capture from PLCs, smart sensors and inline analytics into a manufacturing data historian.
• Advanced analytics to identify subtle parameter interactions that influence quality or throughput.
• Digital twins and simulation to refine operating windows before full-scale runs.

However, smart tools do not change the basics: qualification runs still need clear questions, realistic conditions, good sampling plans and disciplined execution. Analytics can help make better use of the data, but they cannot rescue poorly designed or inconsistently executed runs. A “smart” qualification is still only as credible as its underlying protocol and governance.

14) Implementation Roadmap & Practice Tips

For organisations formalising machine qualification runs, a pragmatic roadmap looks like this:

• Map equipment: identify which machines and lines are critical enough to require formal qualification runs.
• Standardise protocols: develop risk-based templates for OQ/PQ runs that can be tailored by product and line.
• Align with QMS: embed qualification planning, execution and reporting into QMS workflows and change control.
• Digitise execution: execute runs through MES/eBMR where possible, capturing parameters, events and results electronically.
• Leverage data: use results to set control limits, alarm thresholds and realistic OEE targets.
• Establish requalification rules: define clear triggers and responsibilities for future qualification activity.
• Train and review: ensure engineering, QA and operations teams understand the purpose and expectations, and periodically review completed runs for consistency and learning.

The goal is not to make commissioning slower for its own sake; it is to avoid discovering fundamental weaknesses months after go-live, when customers are already depending on the line and any remediation is expensive and public. Good qualification runs are a controlled, front-loaded way to find and fix those weaknesses early.

15) What This Means for V5

For plants running V5, machine qualification runs can be planned, executed and documented across the same platform that manages routine work orders, quality events and traceability. Instead of being a separate stack of protocols and spreadsheets, qualification becomes part of day-to-day system behaviour. Key components include:

• V5 Solution Overview – Frames V5 as the data spine for equipment, process and product lifecycle. Qualification runs executed through V5 generate data that flows naturally into performance dashboards, genealogy, validation and continuous improvement, rather than living in separate validation folders.
• V5 MES – Manufacturing Execution System – Acts as the execution engine for machine qualification runs. Protocol steps can be mapped to guided MES workflows; qualification batches can be flagged in the system; parameters, alarms, samples and in-process checks are captured in real time; and the resulting electronic records can be reused as part of eBMR / DHR evidence without duplicate data entry.
• V5 WMS – Warehouse Management System – Ensures that qualification runs use the correct materials and that resulting product is correctly identified and segregated. Materials for qualification lots can be staged and labelled distinctively via V5 WMS, and finished goods from those runs can be routed to quarantine, stability, scrap or commercial channels according to the protocol conclusions and QA decisions.
• V5 QMS – Quality Management System – Provides the governance layer for machine qualification runs. Protocols, risk assessments, approvals, deviations and final reports can live as controlled QMS records. Trigger rules in V5 QMS can ensure new equipment, significant process changes or major software upgrades cannot go live until machine qualification runs have been executed and approved in line with site policy.
• V5 Connect API – Connects qualification activity in V5 with external tools and data sources: PLCs and OEM systems for high-frequency process data; LIMS for qualification-specific tests; or corporate validation repositories and analytics platforms. Through V5 Connect, customers can feed historian data into V5 MES for contextualisation, or push V5 qualification evidence into corporate validation and audit portals without manual file juggling.

In this model, the glossary concept of machine qualification runs translates into a practical set of V5 configurations and workflows: special work-order types for qualification, guided MES step lists linked to QMS protocols, WMS rules for material and product handling, and APIs for consuming and publishing rich process data. That makes qualification both more rigorous and easier to execute—because it rides on the same V5 backbone the plant already uses every day for production, quality and logistics.

FAQ

Q1. Are machine qualification runs always required before routine use of equipment?
For equipment that materially affects product quality, safety or regulatory compliance, some form of structured qualification run is expected in most regulated and many non-regulated environments. The depth and formality should be risk-based, but relying solely on vendor FAT/SAT or an informal “trial run” is difficult to defend once issues arise.

Q2. Can machine qualification runs use non-commercial or surrogate product?
Sometimes. Early OQ runs may use surrogates or placebo product to demonstrate equipment function and safety. However, final performance qualification and process validation usually require runs on the actual commercial formulation, packaging and materials under realistic operating conditions. Protocols should be explicit about what counts as fully representative.

Q3. Do we need a full set of IQ/OQ/PQ documents for every small piece of equipment?
Not necessarily. A risk-based approach is standard practice. Critical equipment and lines that directly influence CQAs warrant full IQ/OQ/PQ and formal qualification runs. Low-risk devices may be covered by simplified commissioning checks or inclusion within the scope of larger system qualifications. The rationale should be documented in the QMS.

Q4. How often should we repeat machine qualification runs?
There is rarely a fixed calendar requirement. Requalification should be triggered by significant changes (equipment modifications, control-system changes, new high-risk products), adverse events, repeated deviations or risk-based review cycles. Some sites perform periodic challenge runs or capability checks instead of full requalification; the important point is that the strategy is explicit and justified.

Q5. Where should we start if our current practice is “run it and see” without formal qualification?
A practical first step is to identify high-impact lines and products, develop a simple qualification protocol template, and execute one or two structured qualification runs with proper sampling, data capture and review. Use those as exemplars to refine templates, train teams and plug qualification into QMS and MES workflows. Once you have a working pattern on a limited scope, extend it to additional equipment based on risk and business priorities.

Related Reading
• Equipment & Validation: Equipment Qualification (IQ/OQ/PQ) | Process Validation | Cleaning Validation | OEE
• Records & Traceability: Batch Manufacturing Record (BMR) | Electronic Batch Record (eBMR) | Device History Record (DHR) | Traceability & End-to-End Lot Genealogy
• Systems & Governance: V5 Solution Overview | V5 MES – Manufacturing Execution System | V5 QMS – Quality Management System | V5 WMS – Warehouse Management System | V5 Connect API | Manufacturing Data Historian | Quality Management System (QMS) | Change Control | Data Integrity