The paper presents an FPGA based system-on-chip (SoC) solution of an adaptive control for compensation of aging motor parameters of two phase hybrid stepper motors. An accurate controlling behavior of the stepper motor is achieved by the identification and adaption of the controlling parameters. With this solution it is possible, to detect modifications of motor parameters caused e.g. by aging effects. Known and unknown parameters of any stepper motor can be identified. The implemented algorithm can be used for any two phase hybrid stepper motors. For online parameter identification, the least squares method is used. The controlling algorithms and the identification are implemented into a customizable SoC, Microsemi’s SmartFusion FPGA. The current measurements of the system are performed by the analog unit of the SmartFusion. Computing intensive parts are implemented into the hardcore ARM Cortex-M3. The analysis of the encoder and the PWM generator are done by reconfigurable hardware.