The disclosed technology provides thermoplastic polyurethane compositions having non-leaching antimicrobial properties while still maintaining good physical properties, methods of making the same, and articles, including medical devices, made from such compositions. The disclosed technology includes a process of making an antimicrobial polymer composition, where the process includes mixing an antimicrobial additive into a polymeric material; wherein said polymeric material comprises a polymeric backbone made up of urethane linkages derived from a polyisocyanate and a polyol; and wherein said mixing occurs under conditions that result in the breaking of a minority of said urethane bonds resulting in reactive isocyanate groups; and wherein two or more of said reactive isocyanate groups react with said antimicrobial additive to covalently bond said antimicrobial additive into the polymeric backbone of said polymeric material; resulting in an antimicrobial polymer composition.