Stepper motor close to PCB/MCU/ADC
Yes you will likely experience some EMI issues, not from the motor , but rather the wire routing close to other cables.  If you use twisted pairs, for all cables, this can improve it and then add a ground plane between interfering sources and signals.  Ensure your supply is well filtered for low ripple.  AC connection from 0Vdc to earth ground with 10nF film will also improve immunity.

The EMI is not always what you expect with some PWM switching rate but a spurious resonance in the current limiter with an inductive motor load often heard in the audio range.