Display omitted •Plasma polymerization penetration depth into porous media is at least tens of μm.•Deposition rate decreases greatly in wells, the chemistry changes moderately.•Two populations of film-forming species are required to explain the data.•The small sticking probability population allows the large deposition penetration. Understanding the role of substrate geometry is vital for a successful optimization of low-pressure plasma polymerization on non-planar substrates used in bioapplications, such as porous materials or well plates. We investigated the altered transport of film-forming species and properties of the coatings for a cyclopropylamine and argon discharge using a combined analysis of the plasma polymer deposition on flat Si pieces, culture wells, microtrenches, a macrocavity, porous hydroxyapatite scaffolds and electrospun polycaprolactone nanofibrous mats. The aspect ratio of the well structures impacted mainly the deposition rate, whereas the film chemistry was affected only moderately. A large deposition penetration depth into the porous media indicated a relatively low sticking probability of film-forming species. A detailed analysis of microtrench step coverage and macrocavity deposition disproved the model of film-forming species with a single overall sticking probability. At least two populations with two different sticking probabilities were required to fit the experimental data. A majority of the film-forming species (76%) has a large sticking probability of 0.20±0.01, while still a significant part (24%) has a relatively small sticking probability of 0.0015±0.0002. The presented methodology is widely applicable for understanding the details of plasma-surface interaction and successful applications of plasma polymerization onto complex substrates.