We have devised a microfluidic platform that incorporates substrate-laden silica beads for sensing the proteolytic activity of botulinum neurotoxin type A (BoNT/A)-one of the most poisonous substances known and a significant biological threat. The sensor relies on toxin-mediated cleavage of a fluorophore-tagged peptide substrate specific for only BoNT/A. Peptide immobilized on beads is recognized and cleaved by the toxin, releasing fluorescent fragments into solution that can be concentrated at an isolated port via evaporation and detected using microscopy. Evaporative concentration in combination with a specific channel geometry provides up to a 3-fold signal amplification in 35 min, allowing for detection of low levels of fluorophore-labeled peptide-a task not easily accomplished using traditional channel designs. Our bead-based microfluidic platform can sense BoNT/A down to 10 pg of toxin per mL buffer solution in 3.5 h and can be adapted to sensing other toxins that operate via enzymatic cleavage of a known substrate.