Droplet‐based microfluidics allows the generation and manipulation of many independent microreactors (pico‐ to nanoliter volumes) optionally hosting human cells. However, one limitation is that mammalian cells within droplets are not fully accessible from outside. The contents of the plugs cannot be completely exchanged so that washing steps for immunoassays are not possible. Additionally, imaging of cells is difficult because cells move within the volume of the plugs. Here, we present an approach in which droplets are used for the specific delivery of compounds across a 150 μm thick polydimethylsiloxane (PDMS) membrane to cells grown on the opposite side of this thin membrane, resulting in spatially separated, parallelizable assays. As a first application, we used this setup to compartmentalize tetracycline within droplets and incubating them in a long channel for 16 h, after which the plugs were flushed out of the channels. Tetracycline diffused into the PDMS membrane and induced the expression of green fluorescent protein in HeLa cells within a large, freely accessible population in a pattern corresponding to the original positions of tetracycline droplets. This should allow the combination of droplet‐based microfluidics with cell‐based assays requiring long incubation times, studies of cell–cell interactions, and chemotaxis.