In this work antimicrobial polyurethane coatings were prepared aiming at self-stratification. A hydroxyl end-capped liquid oligoester consisting of three equimolar diacids and an excess of 1,4-butanediol has been synthesized by a condensation reaction. A set of quaternary ammonium compounds (QACs) which are well known contact killers, was synthesized via a straightforward quaternization reaction. These synthesized precursors were later covalently bonded to the polymer network by addition of a polyisocyanate crosslinker resulting in antimicrobial polyurethane coatings. Self-stratification was confirmed by dynamic contact angle analysis and X-ray photoelectron spectroscopy. The final films showed strong antimicrobial activity against both Gram-positive Staphylococcus aureus and Gram-negative Escherichia coli type bacteria.