Foams are essential in food applications, but maintaining their stability is challenging. Protein-based nanoparticles are ideal stabilizers for foams. We investigated β-lactoglobulin (β-LG) and used microbial transglutaminase (mTG) to create protein nanoparticles. By analyzing protein structures and using molecular dynamics simulation, we studied how mTG cross-linking affected β-LG at a molecular level. Minimal changes were observed in the secondary and tertiary structures of β-LG in its molten globular state. However, the solvent-accessible area of mTG substrates lysine and glutamine underwent substantial alteration, which increased mTG accessibility. These nanoparticles exhibited a size distribution of 10–40 nm and significantly improved foamability and foam stability compared to native β-LG. This study provides a comprehensive understanding of the relationship between β-LG protein conformation, intermediate-sized features in protein nanoparticles, and macroscopic foam properties, which introduces a new approach for utilizing protein nanoparticles in the food industry.