The genetic bases for the Congenital Disorders of Glycosylation (CDG) continue to expand but an understanding of how glycosylation defects cause patient phenotypes remains largely unknown. Here we combined developmental phenotyping and biochemical studies in a new zebrafish model (pmm2sa10150) of PMM2-CDG to uncover a protease-mediated pathogenic mechanism relevant to craniofacial and motility phenotypes exhibted by mutant embryos. Mutant embryos have reduced phosphomannomutase activity and modest decreases in N-glycan occupancy as detected by MALDI MS imaging. Cellular analyses of cartilage defects in pmm2 sa10150 embryos revealed a block in chondrogenesis that is associated with defective proteolytic processing, but seemingly normal N-glycosylation, of the cell adhesion molecule N-cadherin. The activities of the proconvertases and matrix metalloproteinases responsible for N-cadherin maturation were significantly altered in pmm2sa10150 mutant embryos. Importantly, pharmacologic and genetic manipulation of proconvertase activity restored matrix metalloproteinase activity, N-cadherin processing and cartilage pathology in pmm2 sa10150 embryos. Collectively, these studies demonstrate in CDG that targeted alterations in protease activity create a pathogenic cascade that impacts the maturation of cell adhesion proteins critical for tissue development.