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The study presents the development of a new copolymacrolactone structure based on ethylene brassylate (EB) and squaric acid (SA) with different ratios between comonomers. The new system was tested as a network for essential oils encapsulation. The structure of the copolymers was confirmed by spectroscopic investigations and correlated in interdependence with the comonomers content. The interfacial characteristics of the poly(ethylene brassylate-co-squaric acid) copolymers were determined, and the transition from a moderate hydrophilic surface towards a hydrophobic region by increasing the molar content of SA comonomer was highlighted. The affinity for hydrophobic substances of the synthesised macromolecular compounds was used in a process of encapsulation of thymol (Thy) and carvacrol (CC). The newly prepared bioactive compounds were characterised by in vivo biocompatibility tests, and antimicrobial activity, Minimum Inhibitory Concentration (MIC) and Minimum Bactericidal Concentration (MBC).