Protein nanoparticles (PNPs) present versatile platforms for cargo delivery due to their modularity, biocompatibility, and self-assembled structures. PNPs have benefited greatly from developments in bioorthogonal covalent attachment chemistries, which enable efficient post-translational cargo loading. In this paper, we review recent advancements in bioorthogonal strategies for cargo loading onto PNPs, including methods for chemical functionalization of natural scaffolds and the use of established click chemistries. We also discuss how protein engineering strategies, including genetically encoded ligation systems and non-canonical amino acid incorporation, have conferred even greater specificity and control to cargo loading and delivery. We conclude the review with applications and future directions of PNPs in crop and soil sciences, with insights on their translation to industry and agriculture.