BMW E46 Intake Manifold Gasket Replacement – 1998-2006 3 Series – All Models

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BMW E46 intake manifold
BMW E46 Intake Manifold Gasket Replacement Time – 4 Hours
Repair cost level 1

The BMW Repair Guide used this 2003 325ci for the following article.

Repair Summary
The following article provides detailed instructions on replacing the intake manifold gaskets in a BMW E46 3 series car with the M52 or M54 6 cylinder engine. Even though we have used a 2003 BMW 325ci to perform this installation, this article can be applied to any BMW E46 3 series vehicle with minor modifications to the steps below.

If your 1998-2006 3 series is starting to idle rough and is showing signs of poor acceleration and performance, you may be ready for a BMW E46 intake manifold gasket replacement.

As our wonderful BMW E46’rs slowly reach a geriatric age, it’s a fact of life that parts are going to start failing. Many critical engine components, especially those that comprise the air intake system, are made out of plastic or rubber and are especially prone to failure in the extreme heat of the engine compartment.

The intake manifold gaskets in the E46 3 series are notably susceptible to failing in these brutal conditions. Over time the manifold gaskets become hard and brittle creating vacuum leaks and allowing unmonitored air to enter the engine. This unmonitored air “confuses” your engine control module (DME) and can cause a host of issues from rough idling, dashboard warning lights, and over all poor performance. It seems as though every BMW E46 we bring into the BMW Repair Guide these day needs a complete air intake restoration…including pipes, hoses, valves and gaskets.

Replacing the BMW E46 intake manifold gaskets is not technically difficult, but does involve the removal of a lot of parts. Identifying and marking wire harnesses and connections is very important in this repair; there are a lot of them, and labeling them during disassembly makes putting the car back together extremely easier. There is nothing more frustrating than wasting an hour trying to figure out where a wire connection goes, or “burying” a connection under a bunch of installed parts.

While performing this repair, the BMW Repair Guide strongly recommends replacing the idle control valve and DISA valve. As these two critical parts age, they can cause vacuum leaks and a rough idling engine. Now is a great time to replace them since they will need to be removed for this repair. For more information on replacing your idle control and DISA valves, please refer to our article BMW E46 Rough Idle Repair – 1998-2006 3 Series – M52/M54 Engine.

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1. Intake manifold gaskets (required) – Always use a high quality intake manifold gasket when replacing them in your BMW. Avoid trying to “save a couple bucks” by purchasing a cheap inferior gasket set. We give you several excellent choices below.
2. Throttle body gasket (required)It is standard procedure to replace this gasket every time the throttle is removed from the intake manifold. A fresh gasket for your throttle body is cheap insurance against future vacuum leaks.
3. Intake boot throttle body (optional)The BMW E46 has two intake boots, one that attaches to the throttle and one to the mass air flow sensor (MAF). When the intake boots crack, they let unmetered air into the engine causing error lights and a rough idle. Get ahead of the game and replace your throttle body intake boot during this repair.
4. Intake boot mass air flow sensor (MAF) (optional)The BMW E46 has two intake boots, one that attached to the throttle and one to the mass air flow sensor (MAF). Always replace both of your intake boots together. Since you will be removing them for this repair, now is the time to replace them both.
5. DISA valve (optional) The DISA valve is a common source of vacuum leaks in the BMW E46 3 series. Unfortunately the gasket cannot be purchased separately…you must replace the entire unit. Now is a great time time to install a replacement since it will have to be removed for this repair. We give you several options below based on your budget.
6. Air filter (optional) Keep the engine in your 3 series breathing easier with a fresh air filter. The air filter will need to be removed for this repair, so why not replace it now! Your engine air filter should be changed every 12 months or sooner, depending on your driving conditions.
Section 1 – Removing the BMW E46 intake manifold
  1. Remove the right side engine cover using a pick and a 10mm nut driver as shown below.BMW E46 Intake Manifold Gasket Repair- Remove the engine cover caps. BMW E46 Intake Manifold Gasket Repair- Use a 10mm nut driver to remove the engine cover bolts
  2. Remove the cabin air filter cover by loosening the three twist screws that mount it to the filter housing.
    BMW E46 Intake Manifold Gasket Repair- Remove the cabin filter cover.
  3. Using a torx T30 bit remove the three screws securing the filter housing to the fire wall. Remove the filter housing from the vehicle.BMW E46 Intake Manifold Gasket Repair- Remove the cabin filter housing
  4. Using a T30 torx bit, loosen the two bolts securing the metal bulkhead cover (the bolts are attached to the cover and should not be able to be completely removed). Remove the bulkhead cover from the car.BMW E46 Intake Manifold Gasket Repair- Remove the bulkhead coverRemove the bulkhead cover from the vehicle.
  5. The next step in the BMW E46 intake manifold gasket repair is to remove the air box (intake muffler) from the engine compartment. Use a 10mm nut driver or socket wrench to remove the two air box mounting bolts on the left side of engine compartment.BMW E46 Intake Manifold Gasket Repair - Remove the air box mounting bolts.
  6. Disconnect the Mass Air Flow (MAF) sensor.BMW E46 Intake Manifold Gasket Repair - Disconnect the mass air flow sensor.
  7. Using a flat blade screwdriver, loosen the hose clamp connecting the air intake boot to the air box.BMW E46 Intake Manifold Gasket Repair - Loosen the intake boot.
  8. Remove the air box from the engine compartment.BMW E46 Intake Manifold Gasket Repair - Remove the air box from the engine compartment.
  9. Remove the vacuum line from the intake boot.Remove the vacuum line from the intake boot.
  10. Remove the DISA valve electrical connector. The release spring is on the back side of the connector.BMW E46 intake manifold - remove the DISA valve electrical connection
  11. You will need to remove the DISA valve to get clearance for intake boot removal. Using a T40 torx bit, remove the two screws anchoring the DISA valve to the intake manifold. Grasp the DISA valve and carefully remove.BMW E46 intake manifold BMW E46 intake manifold
  12. Using a flat blade screwdriver, loosen the hose clamp anchoring the top hose of the intake boot to the idle control valve. Pull the top hose off of the idle control valve being careful not to bend or tear it (there is a screw below it we need to get to in the next step).BMW E46 intake manifold - loosen the intake boot hose clamps.
  13. Using a flat blade screwdriver, loosen the hose clamp anchoring the intake boot to the throttle body. Pull the intake boot off of the throttle body and remove from vehicle. You will notice from the photo below we damaged our intake boot during removal. This boot had 140,000 miles on it and ripped apart during removal. If this happens to you, order one from our parts section above.BMW E46 intake manifold - loosen the intake boot hose clampsBMW E46 intake manifold - remove the intake boot from the engine
  14. Disconnect electrical connection to the throttle body. You may need the help of a flat blade screwdriver to get it loose.BMW E46 intake manifold - disconnect the throttle body electrical connectionRemove the connector from the throttle body
  15. Now it is time to remove the engine wiring harness from the BMW E46 intake manifold. Start by removing the top two T40 torx bolts.BMW E46 intake manifold - remove the top bolts anchoring the wiring harness to the intake manifold
  16. Next move down the wiring harness and remove the 10mm bolt using a nut driver or socket wrench.BMW E46 intake manifold - remove the side bolts anchoring the wiring harness to the intake manifold
  17. Next, the lower throttle body mounting bolt must be removed. Use a 10mm socket wrench with extension.BMW E46 intake manifold - remove the lower throtle body bolt.
  18. Finally, remove the 10mm bolt anchoring the engine wiring harness to the idle control valve.BMW E46 intake manifold - remove the final wiring harness bolt anchoring it to the idle control valve.
  19. Gently pull the wiring harness away from the intake manifold so the manifold can be removed without pinching any wires. Tuck it out of the way.
  20. Remove the electrical connector from the idle air control valve and mark with tape.
  21. Remove the fuel tank venting valve by grasping its rubber mount and pulling straight out off of its mounting plate.BMW E46 intake manifold - remove the fuel tank venting valve
  22. Remove the engine vent hose (crankcase breather hose) from cylinder head cover by squeezing sides of spring clip and pulling loose. Be careful with this hose…it is plastic and can easily crack or break off.BMW E46 intake manifold - remove the crankcase breather hose.
  23. Disconnect the VANOS solenoid electrical connector and label.BMW E46 intake manifold - disconnect the VANOS electrical connection
  24. There is an electrical connection on the back of the intake manifold that will need to be disconnected. It is reachable with your hands…use a flashlight and our images below to locate and disconnect. Make sure to label with tape…this is a common connection that many mechanics forget to reconnect (because of its obscure location).BMW E46 intake manifold - locate the rear electrical connection that runs from the intake manifold to the engine blockRear electrical connection that must be removed.
  25. Remove the oxygen sensor connections from their clips on top of the intake manifold. Tuck gently out of the way behind manifold.BMW E46 intake manifold - disconnect the oxygen sensors.
  26. Using a 10mm socket, remove the last three mounting bolts from the throttle body (one of them was already removed in step 17). Remove throttle body from vehicle.BMW E46 intake manifold - remove the last throttle body bolt and remove the throttle body from the vehicle.
  27. You can now gain access to the lower BMW E46 intake manifold mounting bolt. The lower mounting bolt anchors the intake manifold to the engine block. Using a 16mm socket with an extension, remove the lower mounting bolt.Locate the lower intake manifold mounting bolt.BMW E46 intake manifold - remove the lower intake mounting bolt
  28. Remove the dipstick ventilation hose from the bottom of the PCV valve. The hose runs from the PCV valve to the bottom of the oil dipstick…if you don’t remove it, it will break off and require replacement. You can see from the images below, ours was already broken off. If you break yours during disassembly, order a new dipstick ventilation hose here.BMW E46 intake manifold - disconnect the dipstick vent hose.BMW E46 intake manifold - remove the dipstick ventilation hose form the PCV valve.
  29. Using an 11mm socket, remove the nine intake manifold mounting nuts. Note that the nut closest to the fire wall (#9) is difficult to get to…it is hidden behind wiring. Use patience when trying to remove.

    One of the biggest pains when doing a DIY repair is losing nuts and bolts when removing them with a socket wrench. Nothing is more irritating than dropping a bolt into the engine bay, never to find it again! To avoid losing nuts and bolts, especially those in awkward positions, insert a piece of tape in the socket. The tape will securely hold the nut or bolt while extracting it, avoiding an unnecessary trip to the hardware store to try and replace it.

    BMW E46 intake manifold - locate the nine mounting nuts anchoring the intake manifold to the engine head.Remove the intake manifold nuts.
  30. Grasp the intake manifold with both hands and remove from the threaded studs. It may be necessary to GENTLY tap the BMW E46 intake manifold with a rubber mallet to loosen its seal on the engine head. DO NOT hit the intake manifold hard…it is made of plastic and it can crack. If the intake manifold will not pull off of the engine, check to make sure you have removed all of the nuts.BMW E46 intake manifold - Tap the intake manifold gently with a rubber mallet if it is stuck and wont pull loose from the engine head. Pull the intake manifold loose from the threaded studs.
  31. There is one last electrical connection that can only be accessed when the BMW E46 intake manifold is partially removed. It runs from the intake manifold to the engine block near the fire wall. You may need to use a flat blade screwdriver to pry the connection loose while squeezing the release clip (see images below).BMW E46 intake manifold - locate the final electrical connection near the fire wall.

 

Section 2 – Removing and installing the manifold gaskets
  1. Gently prop up the intake manifold so the rubber gaskets can be removed. Be careful when moving the manifold so as to avoid breaking any vacuum pipes.BMW E46 intake manifold - prop up the intake manifold so the old gaskets can be removed.
  2. Use a metal pick to remove the rubber intake manifold gaskets. Avoid using a screwdriver or any tool which may scratch or damage the manifold.BMW E46 intake manifold - use a metal pick to remove the old gaskets
  3. Vacuum off the cylinder head making sure to get all of the loose debris. Also vacuum out the valve ports in case debris has fallen in. Use a soft brush and rag to thoroughly clean the engine head and the BMW E46 intake manifold. It is very important step that the intake manifold and the cylinder head are completely clean to ensure the new gaskets create an airtight seal.Thoroughly vacuum out the cylinder head. Vacuum out the head ports.BMW E46 intake manifold - Clean the intake manifold with a rag. BMW E46 intake manifold - Use a sof toothbrush to remove and debris from the intake manifold

 

Section 3 – Reassembly of the intake manifold

Reassembling the intake manifold ids very straight forward…just follow the above steps in reverse. Make sure the new rubber gaskets are properly seated in the intake manifold before reinstalling. Pay particular attention when mounting the intake manifold back on the engine; the threaded studs can snag the rubber gaskets, pulling them out of alignment. Take your time and move slowly when reinstalling the intake manifold.

Make sure to use the following torque values when tightening down the intake manifold nuts and throttle body bolts.

Intake manifold nuts – 15 Nm (11 ft-lb)
Throttle body bolts – 13 Nm (10 ft-lb)

Repair finished
If you have any questions or comments, please feel free to contact us. And congratulations for Doing It Yourself!
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