Certain naturally occurring proteins consist of a number of subunit building blocks that are capable of self-assembling to form nanoscale particles with highly organized, symmetrical, and homogeneous structures. These protein-based nanoparticles have high surface/volume ratios and other favorable properties, including mono-dispersibility, high stability, low toxicity, biocompatibility, biodegradability, and capacity for easy genetic and chemical modification. Thus, these particles have attracted considerable research attention and have been manipulated for various applications in different fields. This review describes the engineering of existing protein nanoparticles, with a particular focus on scientific advances in diverse applications, including bioassays, molecular imaging diagnostics, drug delivery, biocatalysis, and materials science. In addition, barriers for the widespread industrial use of such nanoparticles and outlook for the design and creation of novel self-assembled protein-based nanoparticles are considered.