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By Valen
#192893
The MPU6050 datasheet clearly states that it is a 3.3 volt device. (Even the link you gave) So there is no reason to think it should not work with a 3.3 volt DUE.

BUT! If the 5 volt Arduino Uno and Mega already damaged it then who knows how it is going to work at 3.3 volt. Absolute maximum ratings are 6 volts. Maybe it worked and seems fine initially at 5 volts. Over time the 5 volts may have degraded it's sensitivity and damaged it.