This study aims to achieve an improved performance in the position control of a permanent magnet synchronous motor(PMSM) driven single link arm, by compensating for load, friction and torque ripple effects. For this purpose, in the first part of the study, an EKF based algorithm is developed to estimate the model uncertainties, assuming a known load. This is used to determine friction effects in addition to the most dominant component of torque ripple. The estimate of model uncertainties is also used for the partial compensation of this term with a basic PD+ controller. Following this procedure, another EKF algorithm is developed to estimate the amplitude of the dominant torque harmonic to be used for the compensation of that ripple component with the PD+ controller, in addition to the compensation of friction and load. The experimental results demonstrate improved performance in the system response with the on-line estimation of the torque ripple with EKF.