ddesousa:
The HC-06 module is being powered by VIN as it disrupts the rest of the module when connected to 3v3. The modules data sheet says it is rated for supply anywhere between 3.6 and 6 VThis is a 3V3 based application. In the end, I will be using a 3.7 V battery to power the mcu and regulate the 3v3 voltage using the on board regulator.
I see two problems here.
First: the voltage of your battery will most of the time be lower than 3.7V so you're really at or under the specified limit for the HC06 module. You better find a Bluetooth module that's designed for 3.3V.
Second: I doubt the regulator on your board has that low a minimum drop-out. I think there are some regulators that indeed do 0.4V but most are above that, and anyway the moment your voltage drops below 3.7V even that 0.4V drop-out gets you below 3.3V.