Protein adsorption is one of the key parameters influencing the biocompatibility of medical device materials. This study investigates serum protein adsorption and bacterial attachment on polymer coatings deposited using an atmospheric pressure plasma jet system. The adsorption of bovine serum albumin and bovine fibrinogen (Fg) onto siloxane and fluorinated siloxane elastomeric coatings that exhibit water contact angles (θ) ranging from superhydrophilic (θ 150°) were investigated. Protein interactions were evaluated in situ under dynamic flow conditions by spectroscopic ellipsometry. Superhydrophilic coatings showed lower levels of protein adsorption when compared with hydrophobic siloxane coatings, where preferential adsorption was shown to occur. Reduced levels of protein adsorption were also observed on fluorinated siloxane copolymer coatings exhibiting hydrophobic wetting behaviour. The lower levels of protein adsorption observed on these surfaces indicated that the presence of fluorocarbon groups have the effect of reducing surface affinity for protein attachment. Analysis of superhydrophobic siloxane and fluorosiloxane surfaces showed minimal indication of protein adsorption. This was confirmed by bacterial attachment studies using a Staphylococcus aureus strain known to bind specifically to Fg, which showed almost no attachment to the superhydrophobic coating after protein adsorption experiments. These results showed the superhydrophobic surfaces to exhibit antimicrobial properties and significantly reduce protein adsorption.