How To Clean Furnace Heat Exchanger? (4 Steps)

Your gas furnace has one heat exchanger if it is an 80% AFUE model. Most of those with an efficiency level of 90% or higher also have a second heat exchanger – the main reason more heat is transferred into your home’s ductwork instead of being lost out the vent.

The two types of heat exchangers are the primary heat exchanger and the secondary heat exchanger. It is important to make sure that your heat exchanger is clean in order for your furnace to operate as efficiently and safely as possible.

Even a small amount of scale or soot build-up will make your gas furnace work harder than necessary, and that puts stress on the equipment and raises your energy bills. For example, if your furnace has 1/16 of an inch of soot build-up in the heat exchanger, your furnace will lose up to 25% of the heat and have a corresponding increase in fuel usage.

In this Pick HVAC furnace information article, you will learn how to clean a heat exchanger and what warning signs to look for that your heat exchangers need to be cleaned.

How to Test a Heat Exchanger for Inefficient (Dirty) Performance

There are a few tests you can do to explore whether your furnace’s heat exchanger is working properly. Below is a list of tests that a professional HVAC technician would possibly do when servicing your primary and/or secondary heat exchanger and looking for a dirty system:

  • The three-step method pro method is used for detecting unacceptable leakage of flue gases through gas furnace heat exchangers – which indicates that not as much of the heat is being transferred, and too much heat is lost because the exchanger is dirty. These are tests best undertaken by a pro, since most homeowners don’t have the tools, instruments or know-how to tackle them.

>Visual inspection with a strong flashlight and a mirror can look for dirt and for cracks in the heat exchanger.

>Check the burner flames with and without the blower operating – a clean heat exchanger will have a strong draw, and the flame will be blue and be pulled into the heat exchanger.

>Trace the gas by using a methane and nitrogen mixture.

  • Use a gas-detection instrument to measure the level of carbon monoxide (CO) that is in the supply air plenum, exhaust flue, or the area around the furnace.
  • Check the pressure in the heat exchanger by using a magnehelic gauge test.
  • Visual Inspection Test- check the entire heat exchanger for cracks in the steel, any discoloration, or soot. The most common areas to check are at any welds or seams.

Steps to Clean a Heat Exchanger

Annual cleaning of a heat exchanger helps ensure that your heating system is operating as efficiently and safely as possible. Cost for an annual cleaning and tuning of the furnace will range from $200 to $300 because cleaning the primary and secondary (if needed) heat exchangers takes several hours. Will you save that much cost in energy? In very cold climates, you probably will. If your heating season is shorter – you use the gas furnace less than 4 months per year – then consider having the heat exchanger cleaned every 2-4 years.

All high-efficiency furnaces have two heat exchangers, a primary and a secondary heat exchanger. To clean the primary heat exchanger, follow the simple steps below:

  1. Turn the power off to the furnace by turning off the breaker at the junction box. Also, turn off the gas or propane by using the shut-off valves.
  2. Remove any dirt or debris from the heat exchanger block by using a wire brush. Also, use the brush to loosen any of the black soot or scale from each chamber in the heat exchanger. A damp cloth with cleaner specifically for gas furnaces, can also be used to remove any soot or scale.
  3. Using a strong shot vac, vacuum the entire block assembly. Then connect the narrow vacuum attachment to clean out all of the loosened debris that is in the chambers of the heat exchanger.
  4. Turn the breaker back on to supply power to your furnace. Also, turn the gas or propane back on. 

By following the steps above, you can effectively clean your furnace’s primary heat exchanger.

How Often Should a Heat Exchanger be Cleaned?

As we noted, it really depends on how heavily the furnace is used.

  • Zones 1 & 2: Every 5 years
  • Zones 3-5: Every 3 or 4 years
  • Zones 6 & 7:  Every 1-2 years

The next time you have your furnace serviced or cleaned, ask the technician for their recommendation regarding how often to clean your heat exchanger.

How Much Does it Cost to Clean Heat Exchangers?

The average cost to hire an HVAC technician to clean a dirty heat exchanger is $200-$300. A thorough cleaning will remove both soot and scale from the heat exchanger tubes. Scale is unwanted particles that stick to the internal surfaces of a heat exchanger. If the scale is not removed, the scale will become harder and inhibit your furnace system from operating as it is intended. More than that, the scaling will also reduce heat transfer, and efficiency will drop. Too much scaling will result in the overheating of the heat exchanger and a rise in operating costs. Scales that have not been removed properly will eventually corrode the heat exchangers. This corrosion will eventually lead to intensive repairs, even a total furnace replacement.

How do I Know if my Heat Exchanger is Clogged?

There are a number of specific clues or signs that your heat exchanger is clogged and in need of a complete cleaning.

  • CO – oh, oh! First, if your carbon monoxide detector is going off or showing higher than normal readings, then there is a good chance that your secondary heat exchanger is clogged and forcing exhaust air back into the furnace where it will leak into your ductwork and space around the furnace (where you should definitely place a carbon monoxide detector).
  • Leaks: Water leaking from the furnace is also a sign that one of your heat exchangers is plugged. This is most common in a high-efficiency furnace because condensation accumulates and must be drained. When the unit is clogged, the moisture leaks instead of properly draining.
  • Stinks: Another clue that you may have a clogged heat exchanger is that there is a strong sulfur or rotten egg smell coming from the exhaust or anywhere near the furnace.
  • Stains: Finally, a sign that the heat exchanger is clogged is dark staining in the drain hose or the condensate pan or line. This means soot has built up and is mixing with the condensate.

What About Cleaning a Secondary Heat Exchanger?

Cleaning and maintenance for the secondary heat exchanger is just as important as cleaning the primary heat exchanger. The signs that your secondary heat exchanger is clogged or needs to be cleaned are very similar to the signs for your primary heat exchanger. Strong smells, higher carbon monoxide readings, and higher than normal energy bills are all clues that your secondary heat exchanger may need to be cleaned or is clogged. Here’s a video on cleaning a secondary heat exchanger. It will help you decide whether it is a job you want to take on.

We have also prepared a page on Plugged Secondary Heat Exchangers and How to Clean Them.

Written by

Rene has worked 10 years in the HVAC field and now is the Senior Comfort Specialist for PICKHVAC. He holds an HVAC associate degree and EPA & R-410A Certifications.

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