A method of controlling an electric motor (motor) includes providing a processor having an associated memory storing a stator resistance (Rs) estimation (RSE) algorithm that is programmed to implement the RSE algorithm to execute steps including injecting a current waveform at an arbitrary frame of reference into the stator using a field-oriented-control (FOC) motor controller including an Id controller and an Iq controller, and measuring current and voltage values from the motor responsive to the injecting. The measured current and voltage values are then transformed into transformed current and voltage values in a d/q coordinate system. The transformed current and voltage values are low pass filtered to generate filtered d/q current and voltage values, and a value for Rs is estimated from the filtered d/q current and voltage values. The arbitrary frame of reference can be a time-varying frame of reference.