6 Aftertreatment System Issues That Can Lead to Costly Repairs

If there’s one thing diesel truck owners dread, it’s aftertreatment system failures. Designed to reduce emissions, aftertreatment systems can be notoriously complex—and when they fail, repairs can cost thousands. Worse yet, ignoring these issues can lead to engine derates, breakdowns, and DOT violations.

Let’s dive into six of the most common aftertreatment system issues that can lead to expensive repairs and how to prevent them.

1. Diesel Particulate Filter (DPF) Clogging – The Root of Many Problems

The DPF (Diesel Particulate Filter) captures soot and other particulates from exhaust gases. Over time, this soot builds up and needs to be burned off in a regeneration process.

Why It Fails:

• Short trips prevent the exhaust from reaching temperatures needed for passive regeneration.
• Defective sensors can misread soot levels and block regenerations.
• Low-quality fuel or excessive idling increases soot buildup.

Consequences:

• Forced DPF regeneration or cleaning
• Severe power loss and engine derate
• Complete DPF replacement, which can cost $3,000+

Prevention Tip: Use high-quality diesel, avoid excessive idling, and allow for long-haul drives to enable passive regen.

2. DEF System Contamination – A Costly Mistake

Your Selective Catalytic Reduction (SCR) system relies on Diesel Exhaust Fluid (DEF) to neutralize nitrogen oxide (NOx) emissions. If DEF is contaminated, your entire aftertreatment system is at risk.

Why It Fails:

• Using poor-quality DEF or mixing it with fuel or water
• Storing DEF improperly, leading to crystallization
• Faulty DEF pumps or injectors causing improper dosing

Consequences:

• Clogged DEF injectors
• SCR failure, requiring expensive repairs ($5,000+)
• Truck going into limp mode

Prevention Tip: Always use certified DEF, store it in sealed containers, and never mix it with other fluids.

3. EGR Valve and Cooler Issues – Overheating and Carbon Build-up

The EGR (Exhaust Gas Recirculation) system reduces NOx emissions by recirculating exhaust gases back into the intake. However, EGR valves and coolers are notorious for carbon buildup and clogging.

Why It Fails:

• Soot and carbon deposits block the valve or cooler.
• Coolant leaks cause internal damage.
• Extreme heat exposure weakens EGR components.

Consequences:

• Overheating leading to head gasket failure
• Poor fuel economy and reduced power
• Complete EGR cooler failure ($3,500+ repair)

Prevention Tip: Regularly inspect and clean the EGR valve and cooler, and monitor coolant levels for leaks.

4. NOx Sensor Malfunction – False Readings, Big Problems

NOx sensors measure nitrogen oxide emissions and relay data to the ECM (Engine Control Module) to regulate DEF injection. A failed sensor can throw false emissions codes, triggering an engine derate.

Why It Fails:

• Sensor exposure to extreme heat and soot
• Electrical faults or software glitches
• Contaminated exhaust affecting sensor readings

Consequences:

• Engine derate, limiting power and speed
• Failed emissions tests, leading to DOT fines
• Unnecessary component replacements due to misdiagnosis

Prevention Tip: Monitor for check engine lights, replace NOx sensors at recommended intervals, and use OEM-quality sensors.

5. SCR Catalyst Failure – A Pricey Component to Replace

The Selective Catalytic Reduction (SCR) catalyst is a key part of your emissions system, breaking down NOx gases. If it fails, your truck won’t pass emissions tests, and your engine may derate.

Why It Fails:

• DEF crystallization clogs catalyst passages
• Contaminated DEF damages catalyst coating
• Excessive soot buildup from upstream failures

Consequences:

• Failed DOT emissions tests
• Truck forced into limp mode
• Expensive SCR replacement ($6,000+!)

Prevention Tip: Keep your DEF system clean, use high-quality fuel, and fix DPF/EGR issues promptly to prevent SCR contamination.

6. DEF Pump and Injector Failures 

The DEF pump and injector control the precise delivery of DEF fluid into the SCR system. If these fail, the entire aftertreatment system stops working properly.

Why It Fails:

• Crystallization from DEF contamination
• Freezing in extreme cold (if the DEF heater fails)
• DEF pump motor burnout due to clogged lines

Consequences:

• Truck enters limp mode due to low DEF pressure
• Blocked SCR system causing further damage
• Pump replacement ($1,500+)

Prevention Tip: Keep DEF filters clean, use proper winter storage, and monitor DEF quality for signs of contamination.

Final Thoughts

Aftertreatment system failures aren’t just frustrating—they can cost thousands in repairs and downtime. Staying proactive with regular maintenance, high-quality DEF, and proper engine operation can help you avoid expensive breakdowns.

Need expert aftertreatment diagnostics in Circleville, OH? Diesel Truck Repair LLC is here to help! Book a service today and keep your truck running clean and compliant.