This is a common question I get from people that want to modify their BMW. Short answer is it can affect your warranty, but not in the manner you may think.
There are many modifications you can do to your vehicle these days some with physical parts and some with software. Any aftermarket parts does not automatically kill your vehicles warranty as most would believe. Only the parts you changed would be considered not covered under the original BMW warranty. In addition, if that aftermarket part causes damage to any other part on the vehicle, then that will also not be covered under the warranty. For example, if you replace your oil cooler thermostat with a different temp rating one and it gets stuck closed and damages the engine; the engine would not be covered from this. This ,of course, is an extreme example.
The most popular modification to any BMW is tuning the engine for more power. Two main ways I see this done, one is flashing the DME (engine control unit) or using a device called a piggy back. When you flash the DME you are installing a modified engine parameters map. BMW has recently started cracking down on people doing this modification. Every time a BMW technician reads out fault memory with factory equipment a data package of the vehicle called FASTA data is sent to BMW. BMW has a team of people who spend all day going through this data to find cars that have been tuned. Once they find a car that has been tuned they will flag the VIN and stop the DME and power train warranty on the vehicle. This basically means your DME and engine are no longer covered under the OEM warranty for any repairs. The rear differential and transmission repairs needed are up to BMW decide if they will cover under the OEM warranty. This is all done automatically by BMW, the dealer personally has no control over this.
Flashing the DME, in my opinion, is the easiest and best option for tuning a BMW.
A piggy back system modifies signals from the engine to the DME to create more power. A lot of tuners use this system because it is basically electronically untraceable beside the physical components installed on the vehicle. In my opinion, since this system uses a physical component more issues can arise from this type of system. I have first hand seen weird fault codes occur and two complete DME failures from this type of system. In a world where BMW is looking for any modifications on the vehicle this system can be left on the car while sending FASTA data since the DME will never sense the modification.
So if you are planning on modifying your BMW, please be aware of the risks involved with what type of mod you are doing. The easiest ones are exhaust, air box, suspension and wheels. Those modifications normally don’t cause any issues. The engine tuning is by far the most risky to do since BMW is looking for it and safety parameters built into the DME software. Don’t worry much about modifying your BMW since if you’re reading this you have already considered it. In summary, just be aware.