Heterojunctions comprising copper thin films and polyimide underlayers are exploited as an important system for generating flexible microelectronic circuit elements. A fully additive‐based chemical method that allows metallization of polyimide films with copper by the in situ reduction of copper ions doped in surface‐modified polyimide precursors is reported. It is shown that dimethylamine borane is a good reducing agent for copper ions initially complexed with carboxylate anions in the hydrolyzed polyimide layers. This reduction allows diffusion of copper ions towards the film surface to form copper thin films, and simultaneously controls the fabrication of interfacial microstructures between the copper and underlying polyimide. The formation of copper thin films and composite layers is elucidated by glow‐discharge optical emission spectrometry depth profiling, scanning electron microscopy, and cross‐sectional transmission electron microscopy studies, and it is shown that the final microstructure at the copper/polyimide interface is dependent upon experimental variables: a larger amount of copper ions incorporated into the modified layers and a higher reduction rate result in the formation of a granular layer containing smaller copper nanoparticles near the film surface. The granular layers thus formed are found to play a critical role in achieving strong adhesion between metal thin films and the substrate, owing to the increased contact area and hence the increased work of adhesion between them. These results have important implications for realizing a novel adhesion scheme between deposited metals and underlying dielectrics based on nanoscale interlocking through metal nanoparticles.