Last Updated on October 13, 2025 by Hafsa J.

Common Nonconformities in FSSC 22000 V6 Audits and How to Avoid Them

If you’ve ever been through a food safety audit, you know the feeling—that mix of confidence, dread, and hoping the auditor won’t dig too deep into that one process that’s still a little shaky.

And under FSSC 22000 Version 6, that pressure is even more real.

I’ve worked with companies that had clean audits one year and major nonconformities the next—not because their system fell apart, but because they didn’t catch the gaps early enough. What I’ve learned? Most audit findings don’t come out of nowhere. They’re signs of habits, oversights, or “we’ll-fix-it-later” decisions that finally caught up.

Version 6 raises the bar on documentation, traceability, food safety culture, and how well your team can demonstrate what they actually do every day—not just what’s written in a binder.

In this post, we’ll break down the most common nonconformities that show up in FSSC 22000 Version 6 audits—based on real-life audits, not just theory. I’ll walk you through why these issues happen, what they look like in the field, and how to prevent them before they become findings.

If you’re prepping for certification or just trying to keep your system tight between audits, this is the guide you’ve been looking for.

Let’s get into it.

Incomplete or Inconsistent Documentation

Let’s start with a big one. If there’s one area that almost always shows up on audit reports—it’s documentation. Not because companies don’t have enough of it, but because what’s written down doesn’t match what’s actually happening on the floor.

I’ve seen beautiful SOPs that look great on paper—but in reality, the operators are doing something completely different. And under FSSC 22000 Version 6, that disconnect is going to get flagged—fast.

What It Looks Like in the Field

• Your procedure says cleaning is done every four hours—but the log shows six

• Your PRP for pest control hasn’t been reviewed in over a year

• Training records are incomplete or inconsistent across shifts

• Documents haven’t been updated to reflect a recent equipment or process change

• Forms are filled out… but always in the same handwriting and pen color

Auditors are trained to spot patterns—and patterns like that raise red flags.

Why It Happens

Let’s be real—it’s not usually about laziness. It’s often a mix of:

• Teams updating procedures in isolation without involving the actual users

• Daily operations evolving while documentation gets left behind

• No formal process to review, approve, or archive outdated documents

• Different shifts doing the same task… differently

Documentation problems rarely come from bad intentions. But they send a message that your system isn’t fully under control.

How to Avoid It

Here’s how to tighten things up—without overcomplicating it:

1. Do a Quarterly “Reality Check” Audit
Pick a few critical procedures and walk the floor with them in hand. Ask: “Is this still what’s happening?” If not, update the doc—or retrain the process.

2. Version Control Everything
Make sure your team is only using the most current version of any document. Archive old ones properly. A “controlled copy” stamp or digital file access system can go a long way.

3. Assign Ownership by Department
Don’t let QA do all the document control alone. Assign specific documents to team leads in maintenance, production, sanitation, etc. They’re closest to the action—and more likely to keep things accurate.

4. Review Signatures and Records Weekly
A quick weekly check on key records (like CCP logs, cleaning checklists, or maintenance verifications) can help you catch missed initials or sketchy backdating early—before the auditor does.

Real Talk

During one audit I supported, the facility had a beautifully organized binder of sanitation procedures—every one of them approved by QA. But when the auditor asked a sanitation team member to explain how they cleaned a certain piece of equipment… the process was totally different.

It wasn’t malicious—it was just outdated. But it still landed as a minor nonconformity.

Moral of the story? If it’s not happening in real life, it shouldn’t be in your documentation. And if it’s happening in real life, it should be documented.

Weak or Superficial Food Safety Culture Evidence

Let’s get one thing straight—auditors are done being impressed by posters and policy statements. FSSC 22000 Version 6 put food safety culture squarely on the audit checklist, and that means your team needs to live it, not just talk about it.

This one can feel a little abstract, and that’s exactly why it trips people up. Culture is harder to measure than cleaning records—but make no mistake, auditors are looking for signs that your company actually values food safety every day, not just during audit week.

What It Looks Like in the Field

• Employees can’t explain how their work affects food safety

• Staff say “we’ve always done it this way” when asked about procedures

• No real discussion of food safety in team meetings or leadership reviews

• Issues are raised… but never acted on

• Leadership isn’t present or engaged in food safety discussions

I’ve seen audits where the paperwork was flawless—but once the auditor started talking to people on the floor, it became obvious that the culture was all surface and no depth.

Why It Happens

Food safety culture issues usually come from:

• A lack of day-to-day leadership visibility on the floor

• Over-reliance on QA to “own” the entire system

• No structured way to measure or track behaviors

• Training that’s technical—but not connected to purpose

• A disconnect between values and operations (e.g., “safety first” but rushing production to meet targets)

The danger? You might not even realize you have a culture gap until someone outside your organization starts asking questions.

How to Avoid It

1. Ask Your Team “Why” Regularly
During walkthroughs or meetings, don’t just check if procedures are followed—ask why they exist. Can your team explain why handwashing, changeovers, or allergen controls matter? Their answers reveal where culture is strong—or where it’s missing.

2. Make Culture Part of Your Metrics
Track how often food safety is brought up in meetings. Review how quickly issues are raised and resolved. Survey staff anonymously on safety practices and communication. These aren’t feel-good gestures—they’re measurable signals of culture.

3. Involve Leadership in More Than Just Sign-Offs
Have your site or department managers join monthly walkarounds. Ask them to lead short toolbox talks. Their presence matters—and it reinforces that food safety isn’t just QA’s responsibility.

4. Celebrate the Right Behaviors
Publicly acknowledge when someone calls out a risk or speaks up during a shift meeting. Positive reinforcement helps build a culture where people aren’t afraid to act.

Real Talk

I once visited a site where the auditor asked three different team members, “How do you help keep the product safe?” One said, “Ask the supervisor.” Another just shrugged. The third gave a textbook answer that clearly came from a training slide—but couldn’t explain it in their own words.

The finding? A weak food safety culture—not because people were doing anything wrong, but because they weren’t engaged with the system in a meaningful way.

Poor Traceability and Recall Readiness

Here’s a question every auditor is going to test, either directly or indirectly:
Can you trace every ingredient, packaging material, and finished product—forward and backward—quickly and accurately?

If the answer is “kind of” or “we think so,” you’ve got a problem.

FSSC 22000 Version 6 doesn’t just want to see that you have a traceability system. It wants to see that it works under pressure—because in a real recall situation, you won’t have hours to figure it out.

What It Looks Like in the Field

• Missing or inconsistent batch records

• Weak linkage between raw materials and final product lots

• Incomplete supplier information or missing COAs

• Unclear records of where products were shipped or distributed

• Recall procedures that exist—but haven’t been tested in years (or ever)

• Staff unable to walk through a mock recall or traceability exercise with confidence

In an audit I supported recently, the team had beautiful product specs and COAs—but when asked to perform a trace-forward on a specific lot of raw nuts, they realized the receiving record had been logged under the wrong supplier. It took two hours to find the right lot number—and the finding was marked as a major nonconformity.

Why It Happens

• Systems are overly manual, fragmented, or dependent on one person

• Mock recalls are skipped or treated as a checkbox exercise

• Records are stored across multiple systems or physical locations

• No clear process for verifying supplier data during receiving

• Traceability isn’t regularly rehearsed under real-world conditions

It’s not about whether you have records—it’s about whether you can use them effectively when it counts.

How to Avoid It

1. Run Realistic Mock Recalls Quarterly
Test your system using a real product, real lot numbers, and a real timeframe. Aim to complete full trace-back and trace-forward within four hours or less (a common audit expectation).

2. Assign Clear Roles for Recall Scenarios
Make sure it’s not just QA who knows what to do. Distribution, sales, and operations should be involved in mock recall drills—and everyone should know who leads, who supports, and who communicates.

3. Check Data at the Point of Entry
Train receiving staff to verify supplier documentation immediately—don’t assume COAs and batch numbers are accurate until you’ve double-checked. Build this into your receiving SOPs.

4. Use a Standardized Traceability Form or System
Whether it’s digital or paper-based, your traceability records should be:

• Easy to access

• Consistently formatted

• Clearly linked to production and shipping records

Bonus tip: Auditors love when you can pull up traceability data within minutes. It shows confidence and control.

Real Talk

Traceability isn’t just about compliance—it’s about protecting your brand if something goes wrong. I’ve worked with companies who thought they were audit-ready, only to discover during a mock recall that they couldn’t trace allergens across production lines. That’s not just an audit issue—it’s a risk to consumers.

If you want to sleep better during audit week (and every other week), make sure your traceability process doesn’t just exist—it works.

Inadequate Monitoring and Verification of Controls

You’ve got your CCPs in place. Your OPRPs are clearly defined. Your sanitation schedules and pest control plans are documented. Sounds solid, right?

But here’s where it can fall apart: Are you actually checking that these controls are working—and can you prove it consistently?

Under FSSC 22000 Version 6, auditors are looking for more than a completed log sheet. They want to see that your monitoring activities are:

• Done correctly

• Done on time

• Verified for effectiveness

• And backed by actual results—not assumptions

What It Looks Like in the Field

• CCP logs filled out but missing time stamps, initials, or corrective actions

• Calibration records that are incomplete—or worse, fabricated after the fact

• PRPs (like cleaning or pest control) marked “done,” but no verification or follow-up

• No trend analysis or review of results over time

• Internal audit reports that never mention weak controls, even when obvious

I once reviewed a facility where the thermometer calibration was documented… but the thermometer model listed didn’t even exist in the facility. It was a copy-paste error from a previous site. The auditor caught it, of course—and the result was a nonconformity that could’ve easily been avoided.

Why It Happens

• Monitoring becomes routine and rushed—people go through the motions

• Verifications are done late or skipped to “catch up”

• One person is responsible for too many checks, leading to oversight

• No clear review process by supervisors or QA

• Data is collected, but no one looks at it until audit time

The issue here isn’t always bad intent. It’s often complacency—the system seems to be working, so no one digs deeper.

How to Avoid It

1. Build Spot Checks Into Daily Routines
Have supervisors or QA do quick verifications—daily or weekly—not just at the end of the month. Random spot checks keep teams accountable and reduce backdating or pencil-whipping.

2. Track and Review CCP and PRP Data Monthly
If you’re not looking at your control data regularly, you’re missing trends. Build a review process into your management or food safety team meetings.

3. Document the Verification—Not Just the Monitoring
A monitoring log alone isn’t enough. Auditors want to see evidence that someone reviewed the record and took action (if needed). Add a column for verification initials or digital sign-off.

4. Don’t Treat Calibration Like a Background Task
Make calibration schedules visible. Track them with due dates, assign responsibility, and flag overdue items. Equipment that isn’t calibrated correctly invalidates your whole control process.

Real Talk

During one audit, the team had filled out all their sanitation logs perfectly—but when asked to show how the effectiveness was verified, they couldn’t produce a single swab result or validation report. The logs looked great… but without proof the cleaning actually worked, it didn’t matter.

That led to a nonconformity—and a real scramble to implement an environmental monitoring plan after the fact.

Monitoring and verification are the backbone of a functional FSMS. If you can’t show that your controls are effective, everything else—your documentation, your training, your culture—starts to look shaky.

Internal Audits That Don’t Go Deep Enough

Internal audits are supposed to be your safety net—the thing that catches issues before an external auditor ever sees them. But too often, companies treat them as routine or low-priority. And when that happens, the audits become shallow, incomplete, or just plain ineffective.

In FSSC 22000 Version 6, internal audits are no longer just a formality. They’re viewed as a direct reflection of your system’s self-awareness and maturity. If your internal audits are weak, expect that to show up in your certification results.

What It Looks Like in the Field

• Internal audit checklists are vague or overly generic

• Same issues show up year after year—but never seem to get fixed

• Internal audit reports are missing details, dates, or clear evidence

• No documented follow-up on findings

• Internal auditors are auditing their own departments—or auditing areas they don’t understand

I once reviewed a site where the internal audit program hadn’t identified a single nonconformity in two years—while the facility was failing sanitation swabs every quarter. That disconnect was a huge red flag for the external auditor.

Why It Happens

• Auditors are under-trained or lack confidence

• Internal audits are rushed or squeezed into “slow weeks”

• People don’t want to document issues that might reflect badly on the team

• There’s no real consequence for weak findings or missed follow-up

• No clear schedule based on risk, past findings, or process complexity

Internal audits shouldn’t be treated like paperwork. They’re practice for the real thing and a key part of continuous improvement.

How to Avoid It

Rotate and Train Your Internal Auditors
Don’t just assign whoever’s free. Choose people from different departments, give them basic audit training, and rotate them across different processes. It brings fresh eyes and reduces bias.

Make Your Audit Checklist Process-Specific
Instead of generic “Is procedure followed?” questions, tailor your checklist to actual activities. For example:

• Are CCPs monitored at the required frequency?

• Can operators explain what happens if limits are exceeded?

• Are cleaning verifications documented for allergen zones?

Don’t Be Afraid to Write Real Findings
Your goal isn’t to make your site look perfect—it’s to improve it. Minor issues? Document them. Repeat issues? Investigate the root cause. External auditors expect you to know where your gaps are—and they respect it when you own them.

Tie Audit Results Into Management Review
If your findings never leave the QA office, you’re missing a chance to drive change. Make sure trends, recurring issues, and action status updates are shared with leadership.

Real Talk

At one facility I supported, their internal audits had flagged pest control gaps for three quarters in a row—but no corrective action was ever implemented. When the external auditor found a live pest device out of service, it was game over. What could have been a minor issue became a major finding because of repeated inaction.

Your internal audit program tells the auditor how well you know your own system. If you’re missing what they can see in a single walkthrough, that doesn’t inspire confidence.

Unclear or Weak Corrective Actions

Let’s say your audit is done. You’ve got a few findings. Not ideal, but manageable.
Now comes the part that separates strong food safety systems from those that just survive audits: how you respond.

Corrective action plans, or CAPs, are supposed to show that you not only fixed the issue, but understood why it happened—and how you’re preventing it from happening again. But what auditors often see instead? Generic, copy-paste fixes that don’t actually change anything.

If you’re submitting weak or unclear CAPs, you’re not just risking certification delays—you’re sending the message that continuous improvement isn’t a real priority.

What It Looks Like in the Field

• CAPs that only address symptoms, not root causes

• Actions marked “complete” with no evidence attached

• No one assigned to own the fix

• Findings that show up again year after year

• Preventive actions that are vague or missing entirely

Example: An auditor flags that allergen verification is inconsistent. The CAP response? “Staff retrained.”
That might sound fine on the surface—but why was the verification missed? Is the procedure confusing? Is the form unclear? Is the training ineffective? Simply retraining isn’t enough if you don’t fix the underlying issue.

Why It Happens

• Teams rush to close findings without investigating

• Root cause analysis is skipped or done superficially

• There’s pressure to look good on paper instead of actually fixing the problem

• Ownership is unclear, so follow-up gets lost

• Corrective actions aren’t verified for long-term effectiveness

The result? The same issues resurface again and again—and your audit history starts to raise questions.

How to Avoid It

1. Always Start with Root Cause Analysis
Use simple but effective methods like the “5 Whys” or fishbone diagrams. The goal isn’t to assign blame—it’s to understand the process failure.

2. Assign a Responsible Person and a Deadline
If no one owns the action, it won’t get done. Assign clear accountability and a realistic, tracked deadline for implementation.

3. Attach Proof of Completion
If your action is to update a form, show the old and new versions. If it’s training, include the attendance sheet. If it’s equipment repair, attach the work order.

4. Verify That the Action Worked
This is the step that gets skipped most often. Don’t just fix the issue—go back and check that the fix is holding up. Auditors want to see the full cycle: identification, correction, prevention, and validation.

Real Talk

I once supported a site that submitted a perfect-looking CAP for a documentation lapse. But during the next audit, the same issue popped up again—because no one had verified if the document control process was actually working. The result? A repeat finding and a major hit to their credibility.

Corrective actions are more than audit responses. They’re your opportunity to prove your system doesn’t just meet the standard—it learns from its mistakes.

Pro Tips from the Field: How to Stay Ahead of Nonconformities

These aren’t just theoretical best practices. They’re hard-earned insights from real audits—what works, what gets noticed, and what makes the difference between an average audit and a smooth, confident one.

Pro Tip #1: Build a Monthly “Audit Pulse Check”
Don’t wait until audit season to check your system’s health. Every 30 days, review one procedure, one set of records, and one process walkthrough. Rotate departments. This keeps documentation fresh and helps uncover issues while they’re still small.

Pro Tip #2: Train Your Team to Answer “Why,” Not Just “What”
Auditors don’t just want to hear what your procedure says—they want to know your team understands why it matters. When operators can explain how their actions protect product safety, it signals a mature, well-trained culture.

Pro Tip #3: Practice Traceability Drills During Low-Stress Periods
Most facilities wait until prep week to test traceability. Don’t. Run a surprise traceability exercise during a regular week and see how fast your team can respond. Then refine it based on what slows them down.

Pro Tip #4: Document “Positive Observations” Too
Internal audits tend to focus only on what’s wrong. But calling out what’s working—like strong CCP monitoring or quick corrective actions—builds morale and reinforces good practices. Plus, it gives you talking points for management review and external audits.

Pro Tip #5: Treat Every Minor Finding as a Window, Not a Wall
Just because something’s labeled “minor” doesn’t mean you can ignore it. Use it as an opportunity to examine your system more closely. A minor issue left unchecked is often the seed of a major one next cycle.

Common Mistakes and FAQs

Even teams with strong systems get tripped up by small misalignments. And when those small issues add up, they can lead to findings that make you wonder, “How did we miss that?”

Let’s talk about the mistakes I see most often—and the questions I’m asked again and again by teams prepping for FSSC 22000 Version 6 audits.

Common Mistakes

Mistake #1: Relying on Surface-Level Food Safety Culture

Posters on the wall and slogans in your policy aren’t enough. If your team can’t speak confidently about their food safety responsibilities, your “culture” will look performative—and auditors will notice.

Mistake #2: Treating CAPs Like a Checkbox

Responding with “staff retrained” or “procedure reviewed” without digging into root causes won’t cut it anymore. Auditors want to see what changed—and how it was verified.

Mistake #3: Not Closing the Loop on Internal Audit Findings

You identified the issue. Great. But if there’s no follow-through—no root cause, no evidence of action, no re-audit—it’s just a record, not a response.

Mistake #4: Letting QA Carry the Entire System

FSSC 22000 requires cross-functional ownership. If QA is doing all the monitoring, training, and verifying alone, your system is at risk the moment one person is unavailable.

Mistake #5: Ignoring Repeat “Minor” Nonconformities

The first time might be minor. The second or third? It starts to look like a systemic issue. Treat recurring problems like the early warnings they are.

Frequently Asked Questions

Q1: What’s the most common nonconformity in FSSC 22000 Version 6 audits?
The top two I see consistently are weak evidence of food safety culture and incomplete traceability or recall readiness. They’re both areas where the gap between paper and practice shows up quickly.

Q2: Can we fix a nonconformity during the audit?
If it’s minor and you can correct it on the spot—with clear evidence—some auditors may accept that. But most still expect a formal corrective action plan, including root cause and follow-up.

Q3: What happens if we get the same finding two years in a row?
Repeat findings tell the auditor that your corrective actions didn’t work—or weren’t implemented. Expect a deeper investigation and possibly a major nonconformity if the issue is significant.

Q4: Can we challenge a nonconformity we disagree with?
Yes, respectfully. Ask for clarification during the audit, and if needed, provide evidence to support your position. If the finding stands, you can follow your certification body’s formal appeal process.

Knowing Your Gaps Is a Strength, Not a Weakness

If there’s one thing I want you to take away from this—it’s that nonconformities don’t mean failure. In fact, when they’re handled the right way, they’re the clearest sign that your system is evolving and improving.

FSSC 22000 Version 6 has raised the bar. It’s not just about checking boxes or surviving the audit day. It’s about showing that your food safety system actually works—because your people understand it, use it, and improve it when things don’t go to plan.

Here’s what strong teams do differently:

• They prepare all year, not just in the month before an audit.

• They invest in their people, not just their paperwork.

• They welcome findings as opportunities, not threats.

• And most importantly—they own their system at every level, not just QA.

If you’ve seen your own challenges in the examples we walked through—good. That means you’re paying attention. Now it’s time to close the gaps before your next audit makes them harder to ignore.

If you’re ready for an outside perspective, practical coaching, or even just a second pair of eyes on your FSMS, I’d be happy to help. At QSE Academy, we’ve helped teams just like yours turn audit anxiety into audit readiness—with practical, proven support that works.

Reach out to schedule a free consultation, or learn how we can help your food safety system stand up to FSSC 22000 Version 6—with confidence.

You’ve got this. And you don’t have to go it alone.