Proteases are key players in plant development and immunity. When and where these proteases act during these processes is difficult to predict from proteomic or transcriptomic data because proteases are tightly regulated by post-translational mechanisms such as processing, phosphorylation and the presence of cofactors or inhibitors. Protease activities can be displayed using activity-based probes that react with the catalytic site of proteases in a mechanism-dependent manner. Plant proteomes have been labeled with probes for caspases, vacuolar processing enzymes, papain-like cysteine proteases, the proteasome, subtilases, prolyloligopeptidases, serine carboxypeptidases and matrix metalloproteases. Here, we review these protease probes with a focus on the specificity determinants that reside in the probe and the detection methods dictated by the reporter tag.