Segmented polyurethane ionomers find prominent applications in the biomedical field since they can combine the good mechanical and biostability properties of polyurethanes (PUs) with the strong hydrophilicity features of ionomers. In this work, PU ionomers were prepared from a carboxylated diol, poly(tetrahydrofuran) (soft phase) and a small library of diisocyanates (hard phase), either aliphatic or aromatic. The synthesized PUs were characterized to investigate the effect of ionic groups and the nature of diisocyanate upon the structure–property relationship. Results showed how the polymer hard/soft phase segregation was affected by both the concentration of ionic groups and the type of diisocyanate. Specifically, PUs obtained with aliphatic diisocyanates possessed a hard/soft phase segregation stronger than PUs with aromatic diisocyanates, as well as greater bulk and surface hydrophilicity. In contrast, a higher content of ionic groups per polymer repeat unit promoted phase mixing. The neutralization of polymer ionic groups with silver or zinc further increased the hard/soft phase segregation and provided polymers with antimicrobial properties. In particular, the Zinc/PU hybrid systems possessed activity only against the Gram-positive Staphylococcus epidermidis while Silver/PU systems were active also against the Gram-negative Pseudomonas aeruginosa. The herein-obtained polyurethanes could find promising applications as antimicrobial coatings for different kinds of surfaces including medical devices, fabric for wound dressings and other textiles.