The present work investigates the effects of an environmentally friendly treatment based on supercritical carbon dioxide (scCO2) on the interfacial adhesion of flax fibers with thermoset matrices. In particular, the influence of this green treatment on the mechanical (by single yarn tensile test), thermal (by TGA), and chemical (by FT-IR) properties of commercially available flax yarns was preliminary addressed. Results showed that scCO2 can significantly modify the biochemical composition of flax fibers, by selectively removing lignin and hemicellulose, without altering their thermal stability and, most importantly, their mechanical properties. Single yarn fragmentation test results highlighted an increased interfacial adhesion after scCO2 treatment, especially for the vinylester matrix, in terms of reduced debonding and critical fragment length values compared to the untreated yarns by 18.9% and 15.1%, respectively. The treatment was less effective for epoxy matrix, for which debonding and critical fragment length values were reduced to a lesser extent, by 3.4% and 3.7%, respectively.