Electromagnetic tracking technology is primarily used for continuous prostate localization during radiotherapy, but offers potential value for evaluation of dosimetric coverage and adequacy of treatment for dynamic targets. We developed a highly automated method for daily computation of cumulative dosimetric effects of intra- and inter-fraction target motion for prostate cancer patients using fiducial-based electromagnetic tracking. A computer program utilizing real-time tracking data was written to (1) prospectively determine appropriate rotational/translational motion limits for patients treated with continuous isocenter localization; (2) retrospectively analyze dosimetric target coverage after daily treatment, and (3) visualize three-dimensional rotations and translations of the prostate with respect to the planned target volume and dose matrix. We present phantom testing and a patient case to validate and demonstrate the utility of this application. Gamma analysis of planar dose computed by our application demonstrated accuracy within 1%/1 mm. Dose computation of a patient treatment revealed high variation in minimum dose to the prostate (Dmin) over 40 fractions and a drop in the Dmin of ≈8% between a 5 mm and a 3 mm PTV margin plan. The infrastructure has been created for patient-specific treatment evaluation using continuous tracking data. This application can be used to increase confidence in treatment delivery to targets influenced by motion.