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Hold the reset line of the MCU active until the power has stabilized. Design your circuit hardware so that the reset state of the MCU does not produce undesired results.
Without more specifics, there is no way for me to be more specific.
Most hardware takes care of this for you. For example, most PIC microcontrollers pins are in high impedance mode when in reset and remain so coming out of reset. They only change state once the code turns the pin into an output.
You STILL haven't told me which 32bit processor you are using.