We report the high-throughput fabrication of transparent elastomeric monoliths containing customized micropatterns of microcapsules, which might be used as highly flexible identity tags, sensor elements, and photochromic, photonic, or phononic systems. High-throughput replication molding of microsphere monolayers used as sacrificial primary templates via negative secondary replicas and positive tertiary replicas yielded elastomeric specimens containing dense hexagonal arrays of open spherical microcavities. In a subsequent inkjet printing step, some of the open-spherical microcavities were filled with functional materials such as dyes. The subsequent addition of an elastomeric cover layer led to encapsulation of the dyes trapped in the printed microcavities, while empty microcavities were filled with elastomer and vanished.