Multiplexing, i.e., the application and integration of more than one ink in an interdigitated microscale pattern, is still a challenge for microcontact printing (μCP) and similar techniques. On the other hand there is a strong demand for interdigitated patterns of more than one protein on subcellular to cellular length scales in the lower micrometer range in biological experiments. Here, a new integrative approach is presented for the fabrication of bioactive microarrays and complex multi-ink patterns by polymer pen lithography (PPL). By taking advantage of the strength of microcontact printing (μCP) combined with the spatial control and capability of precise repetition of PPL in an innovative way, a new inking and writing strategy is introduced for PPL that enables true multiplexing within each repetitive subpattern. Furthermore, a specific ink/substrate platform is demonstrated that can be used to immobilize functional proteins and other bioactive compounds over a biotin–streptavidin approach. This patterning strategy aims specifically at application by cell biologists and biochemists addressing a wide range of relevant pattern sizes, easy pattern generation and adjustment, the use of only biofriendly, nontoxic chemicals, and mild processing conditions during the patterning steps. The retained bioactivity of the fabricated cm2 area filling multiprotein patterns is demonstrated by showing the interaction of fibroblasts and neurons with multiplexed structures of fibronectin and laminin or laminin and ephrin, respectively.