Magnetic micro- and nanoparticles (MPs)-based composite materials are widely used in various applications in electronics, biotechnology, and medicine. This group of silicone composites have advantageous magnetic and mechanical properties as well as sufficient flexibility and biocompatibility. These composites can be applied in medicine for biological sensing, drug delivery, tissue engineering, and as remote-controlled microrobots operating in vivo. In this work, the properties of polydimethylsiloxane (PDMS)-based composites with different percentages (30 wt.%, 50 wt.%, 70 wt.%) of NdFeB microparticles as a filler were characterized. The novelty of the work was to determine the influence of the percentage of MP content and physiological conditioning on the properties of the PDMS-MP composites after in vitro incubation. An important essence of the work was a comprehensive study of the properties of materials important from the point of view of medical applications. Materials were tested before and after conditioning in 0.9 wt.% NaCl solution at a temperature of 37 °C. Several studies were carried out, including thermal, physicochemical, and rheological tests. The results show that with an increase of the incubation time, most of the measured thermal and physicochemical parameters decreased. The presence of the magnetic filler, especially at a concentration of 70 wt.%, has a positive effect on thermal stability and physicochemical and rheological properties. The performed tests provided important results, which can lead to further research for a broader application of magnetic composites in the biomedical field.