Combining magnetic nanoparticles (MNPs) with high-voltage processes to produce ultra-thin magnetic nanofibers (MNFs) fosters the development of next-generation technologies. In this study, polycarbonate urethane nanofibers incorporating magnetic particles were produced via the electrospinning technique. Two distinct types of magnetic payload were used: (a) iron oxide nanoparticles (IONPs) with an average size and polydispersity index of 7.2 nm and 3.3%, respectively; (b) nickel particles (NiPs) exhibiting a bimodal size distribution with average sizes of 129 nanometers and 600 nanometers, respectively, and corresponding polydispersity indexes of 27.8% and 3.9%. Due to varying particle sizes, significant differences were observed in their aggregation and distribution within the nanofibers. Further, the magnetic response of the IONP and/or NiP-loaded fiber mats was consistent with their morphology and polydispersity index. In the case of IONPs, the remanence ratio (M/M) and the coercive field (H) were found to be zero, which agrees with their superparamagnetic behavior when the average size is smaller than 20-30 nm. However, the NiPs show M/M = 22% with a coercive field of 0.2kOe as expected for particles in a single or pseudo-single domain state interacting with each other via dipolar interaction. We conclude that magnetic properties can be modulated by controlling the average size and polydispersity index of the magnetic particles embedded in fiber mats to design magneto-active systems suitable for different applications (i.e., wound healing and drug delivery).