Arabidopsis thaliana encodes 56 subtilisin-like serine proteases (subtilases), and some are involved in the proteolytic processing of plant peptide hormones. Here, we have investigated the role of one subtilase, AtSBT5.4, in whole plant physiology by examining gain- or loss-of-function phenotypes. Knockouts of AtSBT5.4 had no apparent phenotype; however, overexpression produced a clavata-like phenotype with fasciated inflorescence stems and compounded terminal buds. Production of the phenotype depended on the enzymatic activity of the subtilase, because substitution of serine at the active site abolished the overexpression phenotype. When AtSBT5.4 was overexpressed in a clavata3 mutant background, a novel phenotype was produced suggesting that AtSBT5.4 interacts with the clavata signaling pathway. However, AtSBT5.4 did not cleave CLAVATA3 (CLV3) or a fluorogenic peptide representing the putative cleavage site in CLV3 under in vitro conditions suggesting that the interaction in vivo does not involve the cleavage of CLV3. Overexpression of AtSBT5.4 in a wuschel (wus) background suppressed the AtSBT5.4 overexpression phenotype indicating that WUS function is required for the AtSBT5.4 overexpression phenotype.