Sensitive, inexpensive, and rapid protease activity assays are of great merit for clinical diagnostics. Detection of protease-based toxins produced by Clostridium botulinum and Bacillus anthracis represents a particularly challenging task, as exceptional sensitivity is a prerequisite because of the extreme potency of the toxins. Here we present an inexpensive and sensitive assay platform for activity-based protease quantification utilizing filamentous bacteriophage as an exponentially amplifiable reporter and its application to the detection of these bacterial toxins. The assay is based on specific cleavage of bacteriophage from a solid support and its subsequent quantification by means of infectivity or quantitative PCR. Detection of botulinum neurotoxin (BoNT) serotypes A and B and anthrax lethal factor in the picomolar range was demonstrated with a limit of detection of 2 pM for BoNT/A under optimized conditions.