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Biotechnology is increasingly relying on high-throughput experiments in which large populations of cells are phenotyped and selected based on performance, e.g., for producing a desired product. Droplet microfluidics enables high-throughput screening, and as such, it lends itself ideally to such experiments, but reliance on a fluorescent readout is limiting. Herein, we report a system integrating droplet electrospray ionization–mass spectrometry (ESI-MS) with a microfluidic voltage-mediated droplet printer to enable online analysis and capture of cell-containing aqueous droplets, ultimately offering the possibility for label-free phenotyping and selection of cells. Escherichia coli (E. coli) cell-containing droplets (20 nL) are split into two volume fractions within a microfluidic splitter chip. One fraction is analyzed using a sheath-flow ESI source with MS, while the sibling fraction is printed onto an agar plate using a custom-built voltage-mediated microfluidic printer. Printed droplets can grow into single microbial colonies that map back to their respective droplet ESI-MS signal with 94–99% accuracy and without carryover. Nearly synchronous and stable system operation is shown for infusion rates in the range of 0.4–1.2 droplets/s, while the achieved droplet spacing and printing precision can enable reliable single-colony retrieval for further analyses or gene sequencing. The system is also shown for phenotyping and selection of an E. coli variant engineered to produce l-lysine among control cells. The method enables screening cell colonies for chemical composition and collecting them for further processing with potential application in synthetic biology and enzyme engineering among others.