The E90 is one of my favorite vehicles I have ever owned. The handling is amazing, they have significantly more space than my old E36, and maintenance costs are reasonable. Although, this article will focus on common problems with the BMW E90 (and there are quite a few), I want to remind you early on that I consider these vehicles to be quite reliable overall.
You can read my full E90 review here, this article will discuss the E90’s most common problems, symptoms, and repair costs.
Oil Leaks
Valve cover gasket & oil filter housing gasket 
I’m not going to get into these two common issues too deeply because both of these leaks are not just common on E90s, they are extremely common on every 3 Series I have ever owned. E36s, E46s, E90s, and F30s all commonly have these leaks.
Valve cover gaskets are cheap and easy to replace. It was one of the first DIYs I did, and it can save you some money to do yourself.
Symptoms typically include 1) leaking oil on the side of the head, 2) potentially a burning oil smell, and 3) in worst-case scenarios you may have smoke coming from the engine bay. If there is smoke, it is caused by oil dripping onto the exhaust manifold and then burning off.
Oil filter housing gaskets are a little more difficult to replace but are still within the scope of a beginner.
Symptoms are significantly less noticeable than the valve cover gasket but sometimes you will have 1) oil leaking on to the front of the engine, and/or 2) oil leaking down the driver’s side of the engine block.
Oil sludge in the Vanos solenoid
The Vanos itself is pretty reliable on the E90, but these vehicles utilize two Vanos solenoids. Vanos solenoids control the flow of oil to the cam gears, allowing the timing to adjust. They sometimes get clogged with oil sludge, and this can cause a severe impact on horsepower, lack of lowered torque, and a check engine light.
Luckily the Vanos solenoids are very easy to remove and clean out or replace, and if you need to replace them the parts are relatively inexpensive.
N54 twin-turbo
Twin-turbo failure on the early model E90s with the N54 engine is infamous. A sign that your turbo is soon to fail is a wastegate rattle, and replacing the turbos is RIDICULOUSLY expensive. The turbochargers typically get replaced because of a faulty wastegate.
Wastegate rattle does not always mean that the turbochargers need to be replaced, in fact many owners have been able to adjust their turbo wastegates and get rid of the rattle.
Symptoms of turbocharger failure include 1) engine rattling noise, 2) low boost engine code, 3) smoke coming from the exhaust, and 4) a loss of power.
The turbochargers alone cost around $800 a pop and labor can cost several thousand dollars!
High-Pressure Fuel System
High-Pressure Fuel Pump (HPFP)
The BMW E90 utilizes a high-pressure fuel system, which requires a high-pressure fuel pump to inject fuel into the engine. When this fuel pump becomes faulty your E90 wont get the proper air-fuel mixture that it needs.
Unfortunately, the high-pressure fuel pump is easily one of the most common problems on early E90s with the n54 engine, and the pump is also expensive to fix.
BMW realized that its pumps were problematic after a class-action lawsuit, and they were warrantied for 120,000 miles or ten years. At the time of this writing it is 2020, so any n54 on the road has likely already had its fuel pump replaced at least once before.
Symptoms of a bad pump include a 1) check engine light, 2) long crank time, and 3) the car is in limp mode, and runs poorly with decreased power.
If you are looking to DIY this replacement be forewarned that the intake manifold must be removed. Although intake manifold removal is not the most difficult job on an E90, I do not recommend it to beginners.
Labor costs for the fuel pump replacement run well over $1,000, but as I mentioned previously, it’s likely that your fuel pump has already been replaced at least once before.
Fuel Injector Problems
The N54 engines used a different fuel injector maker than the N55s. Unfortunately, these injectors are considerably more problematic than the N55 injectors. The seals inside of the injectors will frequently deteriorate over time and this will cause fuel leakage.
Symptoms of fuel injector failure include 1) engine misfiring, 2) rough idling, 3) and a check engine code. Fuel injectors are not cheap, they cost over $1,000 just for the parts.
BMW replaced the N54 injectors because it found they were too expensive, less reliable, and offered little benefit over cheaper Bosch fuel injectors.
Water Pump Failure 
I owned two BMW E36s for several years, and that generation was notorious for water pump issues. Actually, the coolant system in general was notorious for leaving you on the side of the road with a blown head gasket if you did not follow the recommended replacement interval to a tee.
The E90 water pumps are worse in my opinion. Sure, the E36s had stock plastic impellers, but all you had to do was replace it with the metal impeller and you would not hear another peep out of the water pump.
The E90 water pumps are electronic and during the best of times they work pretty well. But when they fail they rarely give you much of a heads-up before they do, which is why I recommend that you have these pumps replaced preventively. Nobody wants to be left on the side of the highway because their water pump went out.
Symptoms of a failing/failed water pump include: 1) engine overheating, 2) fan comes on immediately even when the engine is cold, 3) and possibly a check engine light.
The E90 electric water pump is not a cheap piece of equipment. A replacement will cost around $400, and labor is several hundred more. E90 water pump replacement is more difficult than on previous models, but a dedicated DIYer can get the job done in several hours.
Carbon Buildup 
This is a ridiculous problem that I had never been faced with until I purchased an E90. The carbon buildup problems in E90 n54s are because of the direct fuel injection systems that they use. Direct fuel injection certainly has some advantages over manifold injection systems, but one of the big drawbacks is the carbon buildup.
This is a problem on ALL direct injection systems, not unique to BMW. The fuel injectors inject fuel directly into the combustion chamber. Manifold injection injects fuel into the intake manifold.
So why does this make a difference? The injectors do not shoot the intake ports or the valves with gasoline so they do not get cleaned by the gasoline. This causes carbon buildup inside the ports and on the valves.
Turbo-charged direct fuel injection engines need to be walnut blasted from time to time to prevent too much carbon accumulation. The typically recommended interval in 40-50,000 miles, but I have been told that the n55s require less maintenance in this area than the n54s. One benefit you will notice if your ports were heavily clogged is a horsepower increase. Some people have reported increases of up to 20 horsepower. Of course, this is horsepower you are getting back, not new horsepower.
Walnut blasting basically is where a technician will shoot a mixture of pressurized air and walnut shells into the intake ports in order to clean the carbon deposits.
Walnut blasting usually costs about $250-$300 depending on the area you are in.
Here are some tips on reducing/preventing carbon buildup.
1) Use BMW fuel system cleaner every 5-10,000 miles. Even though this will not wash over the valves, it will help by preventing your injectors from becoming fouled.
2) Change your oil every 7,500 miles or less, and change it with good quality oil!
Faulty steering wheel lock
One of the more annoying E90 issues a faulty steering wheel lock. Many people have reported issues where they will insert the key into the ignition, the dash illuminates the red steering lock symbol, and the car won’t start.
Sometimes people can get the car to start by wriggling or reinserting the key, however, eventually the wheel lock will fail completely and you will have to have the vehicle towed to the dealership.
When this issue initially arose years ago BMW was replacing the entire steering column. In recent years, however, this issue has been able to be resolved by simple software updates or computer resets.
Conclusion
These various issues might be making you think twice about purchasing an E90, but I want to remind you that I am only compiling a variety of known issues with the E90.
The vast majority of E90 owners enjoy their vehicles and may only have a few of these issues over the lifetime of the car, and I would argue that the E90 is one of the best used 3 Series BMWs you can purchase right now. I have owned my E90 328i for more than a year, it has well over 100,000 miles and I have enjoyed it tremendously.