In this work, magnetic functionality was introduced to cross-linked acrylamide-based particles via the in situ coprecipitation of iron oxide nanoparticles within the hydrogel particle interior. Cibacron Blue F3G-A was then incorporated onto the magnetic hydrogel scaffold to facilitate the harvest of targeted protein species. The dye-loaded magnetic particles were physically characterized, and their protein sequestration performance was investigated. The results of these studies indicated that dye-loaded magnetic particles sequestered a greater amount of lower molecular weight proteins from the test solution than was achieved using reference particles, dye-loaded cross-linked N-isopropylacrylamide-based core-shell particles. This difference in protein harvesting ability may reflect the higher degree of dye-loading in the magnetic particles relative to the dye-loaded core-shell particles.