Atomic force microscopy (AFM) imaging and force-distance curves have been used to investigate, in situ, the nanoscale organization of collagen adsorbed on polymer substrata covering a wide range of surface roughness and surface hydrophobicity: bisphenol A polycarbonate (PC), poly(ethylene terephthalate) (PET), and poly(vinylidene difluoride) (PVdF) used as such or treated by an oxygen plasma discharge (ox). After collagen adsorption, PC and PCox showed patterned structures under water, the size of which was influenced by substratum surface oxidation. These structures are attributed to aggregated ends of collagen molecules. Extended rupture lengths were observed in the force-distance curves, suggesting that bundles of collagen molecules adhere to the AFM probe and are progressively torn out upon probe retraction. In contrast, on PET, PETox, PVdF, and PVdFox, adsorbed collagen formed a smooth, homogeneous film devoid of any topographic feature, and no extended rupture lengths were observed. After drying, holes in the collagen film were observed on PET and PVdF and not on PETox and PVdFox. The influence of substratum roughness and physicochemical properties is discussed, considering the mobility of collagen molecules at the interface.