We delineate the interconnected human protein substrate landscape of 3CLpro using Terminal Amine Isotopic Labeling of Substrates (TAILS) analysis of human lung and kidney cells treated or not with interferons (N = 12), supported by analyses of SARS-CoV-2-infected human lung cells. FragPipe analysis of non-enriched samples (preTAILS) revealed ~25% of the substrates validated by two different N-terminomics methods. Large numbers of neo-C-termini in preTAILS samples double-validated cleavage sites identified by N-TAILS. Synthetic peptide cleavage kinetics for each cleavage site in >250 substrates ranked substrate cleavage events and with PICS analyses enabled the rational design of improved peptide cleavage assays. Molecular docking simulations of 3CLpro engaging substrates confirmed that ~10% of validated sites were noncanonical that diverged from SARS-CoV (-1) to guide substrate specificity. Protein-protein interaction analysis shows that cleavage by 3CLpro of the interactors of essential effector proteins effectively strands these from their binding partners and so amplifies the consequences of proteolysis throughout the cell by protein complex disassembly and remodelling. Using recombinant protein digestion, Edman degradation, and digestion of normal human bronchial epithelial cells, we further confirmed substrate cleavages. We show that 3CLpro targets multiple proteins in the Hippo pathway, including galectin-8 and MAP4K5, key transcription effectors, mRNA processing and translation. Thus, new mechanistic insight into novel mechanisms of evasion of antiviral host cell immunity, hijacking of the host cell proteins, and disruptions in cell shape and syncytium formation was enabled by rationale start points identified in the 3CLpro substrate degradome. The Atlas of CoV-2 substrates establishes a foundational resource to accelerate further exploration of SARS-CoV-2 pathology in the COVID-19 cellular coup d’etat.