•Functional plasma polymer was prepared on electrospun polymer nanofibrous mat.•Plasma polymerization run at atmospheric pressure in Ar/maleic anhydride/C2H2 mixture.•Anhydride/carboxyl plasma polymer thin films coated uniformly the polymer nanofibers.•The coating penetrated deep into the nanofibrous mat. This work investigates for the first time the penetration depth, nanoscopic homogeneity and conformality of the plasma polymerization onto an electrospun nanofibrous mat. The study is carried out on the model example of atmospheric pressure plasma co-polymerization of anhydride-rich films onto polycaprolactone mats that can find a significant practical applications, for example in tissue engineering and regenerative medicine. Since the surface-to-volume ratio of nanofibrous mats is enormous and the structure of mats resembles extracellular matrix the successful plasma coating of each whole fiber and understanding the penetration of the polymerization into the mat structure are extremely important. The films with reactive anhydride groups were prepared by co-polymerization of maleic anhydride and acetylene using dielectric barrier discharge. The studies were accompanied by the quantification of anhydride groups directly on the PCL electrospun mat using the chemical derivatization with trifluoroethylamine and X-ray photoelectron spectroscopy. The nanoscopic homogeneity and conformality of the anhydride plasma polymer coating on the front side and backside of the nanofibrous mat, 30–40 μm in thickness, did not differ according to the dynamic SIMS mapping. The films containing approximately 6 anhydride groups per 100 carbon atoms coated homogeneously the nanofibers deeper in the PCL mat. The characteristic penetration depth of the deposition was estimated as 46 ± 5 μm.