Mechanical noise is caused by the physical components in the structure of the stepper motor. Common examples contributing to noise include unsecured mounting structures, bent shafts, and loose or no bearings. All of these examples cause unnecessary vibrations and resonant frequencies to appear. Other mechanical noise factors include motor housing, balance of rotor, and bearing choice.

The motor housing structure has a significant effect on high speed motor applications. If the rotor is out of balance, there will be a spike in frequency directly related to speed of the motor. Electric motors use several types of bearings: sliding sleeve bearings or rolling bearings. Sleeve bearings are generally considered to be quiet bearings. A properly lubricated sleeve bearing will only produce very high noise frequencies due to the bearing and shaft finish. Rolling bearings are generally considered to be noisy and have many factors that can lead to a noisy outcome.

Most mechanical noise can be minimized by stiffening the mounting structures and choosing noise dampening materials - such as mounting the motors in sound absorbing materials like rubber, balancing the rotor, and using properly maintained bearings.