The development of materials with antifouling properties is crucial in many areas, including medicine and food packaging. In this study, 2D-matrices made of polylactic acid (PLA), polyhydroxybutyrate (PHB), or polyhydroxybutyrate-co-valerate (PHB-HV) were surface functionalized through aminolysis with three polyfunctional amines, 1,6-hexamethylenediamine (HDA), tetraethylenepentamine (TEPA), and polyallylamine hydrochloride (PAH). The aminolysis procedure was thoroughly studied to ensure a high amount of amine groups while preserving the structural properties of the films. Interestingly, PHB and PHB-HV were found to be more sensitive to aminolysis than PLA, and the highest amino group density was achieved in surfaces etched with PAH. A decrease in the contact angle from ca. 85° to ca. 70° was revealed for polymers functionalized with HDA and TEPA and a drastic reduction in Staphylococcus epidermidis adhesion was observed for PHB-HV functionalized with the polymeric amine PAH. Polymer antimicrobial activity was found to be related to the degree of surface functionalization. The functionalized, cationic polymer surfaces were supposed to act upon contact with bacteria, without releasing any antimicrobial agent. The developed bioactive surfaces may have potential applications as flexible films for food packaging.