Integrating interfacial molecular nanolayers (MNL) with inorganic nanolayers is of interest for understanding processing-structure/chemistry correlations in hybrid nanolaminates. Here, we report the synthesis of Co/biphenyldithiol (BPDT)/Co nanolayer sandwiches by metal sputter-deposition and molecular sublimation. The density and surface roughness of the Co layers deposited on the native oxide are invariant with the Ar pressure pAr during deposition. In contrast, the Co layer roughness rCo deposited on top of the BPDT MNL increases with pAr, and correlates with a higher degree of Co oxidation. Increased roughening is attributed to MNL-accentuated self-shadowing of low mobility Co atoms at high pAr, which consequently increases Co oxidation. These results indicating MNL-induced effects on the morphology and chemistry of the inorganic layers should be of importance for tailoring nanolayered hybrid interfaces and laminates.