Cysteine cathepsins proteases are enzymes that play essential physiological roles, but their activity is also associated to different aspects of cancer progression and to the development of other diseases. Therefore, cysteine cathepsins are relevant and promising therapeutic targets, yet no cathepsin inhibitor has gained regulatory approval to be used as anti-cancer drug or for any other medical purpose. In this thesis, I describe the design, development and testing of non-natural peptide inhibitors (NNPI) of cysteine cathepsins. The initial design of the inhibitors was inspired by the structure of a natural substrate of cathepsin S (CTSS), and an electrophilic group capable to react with the cysteine in the active site of cathepsins was integrated to the molecular structure to obtain NNPIs able to covalently inhibit their targets. To identify structural modifications that could improve the potency and specificity of NNPIs, we designed and performed single-site mutagenesis screenings that eventually led to the development of four new cathepsin inhibitors having high affinity and specificity for their targets, namely CTSS, CTSB, CTSK and CTSL. Since systemic inhibition of these targets can induce deleterious side effects, we conjugated the NNPIs with multiple specific antibodies, thereby creating a modular antibody-based platform for cell type-specific delivery of cathepsin inhibitors. Antibody-peptide inhibitor conjugates (APIC) were then tested in cellular assays: we demonstrated that they reach the cellular compartment of interest (the lysosomes) and achieve inhibition of their target cathepsins in cancer cells as well as in primary B cells and osteoclasts. Finally, we showed that APIC-mediated inhibition of CTSB hinders breast cancer cells invasiveness in vitro, and CTSS inhibition is effective in mediating lymphoma cell killing in vitro and vivo through the activation of CD8+ T cells. In conclusion, this thesis describes a drug development strategy to efficiently identify selective cathepsin inhibitors and specifically deliver them to target cells through antibody conjugation. Our approach can be generalized to inhibit a broader class of proteases for the treatment of cancer and other diseases.