Imidazolium-based ionic liquids (ILs) have interesting antimicrobial activity and their inclusion in a flexible film is ideal to take advantage of their properties in practical applications. Poly(ether-block-amide) (Pebax®Rnew) films were prepared by solution casting, loading two synthetized ILs (1-hexadecyl-3-methylimidazolium dimethyl-5-sulfoisophthalate [Hdmim][DMSIP], IL1 and 1-octyloximethyl-3-methylimidazolium hexafluorophosphate [OOMmim][PF6], IL2) up to 5 wt.%. The ILs were characterized by 1H NMR and MALDI-TOF spectroscopy. The films were investigated for miscibility, morphology, wettability, spectral properties and gas transport. The films display a good thermal stability (>200 °C). Differential scanning calorimetry (DSC) proves phase separation in the blends, that is consistent with FTIR analysis and with the island-like surface morphology observed in the micrographs. Gas permeability tests revealed that the IL-loaded films are dense and poreless, keeping the selectivity of the polymer matrix with a somewhat lessened permeability owing to the impermeable ILs crystals. The film antimicrobial activity, evaluated against Gram-negative and Gram-positive bacterial strains, was correlated to the structure of the incorporated ILs. The smaller IL2 salt did not modify the hydrophobic nature of the neat polymer and was readily released from the films. Instead, IL1, having a longer alkyl chain in the cation, provided a promising antimicrobial activity with a good combination of hydrophilicity, permeability and thermal stability.