Bacteria living on surfaces are often confined to droplets. When these droplets evaporate, the motion of the liquid-air interface and the associated internal capillary flow confine the bacteria. Here we study how E. coli bacteria interact with this capillary confinement and agglomerate at the droplet’s contact line. Counter-intuitively, the bacterial activity does not cause the bacterial patterns to homogenize. Instead, a non-trivial self-organization of bacteria arises that causes a persistent local stirring of the liquid. We demonstrate that, depending on the droplet’s ambient conditions, this bacterial collective motion gives rise to an instability in bacterial number density that leads to the formation of a fingering pattern. By a combination of experiments and theoretical modelling, we investigate how the bacterial motility, number density and droplet evaporation rate control the pattern dynamics. Ultimately, our aim is to understand how the interplay between the bacteria and their surrounding liquid governs their dispersal.