The impact of engineered nanomaterials intentionally or incidentally released in the environment on photosynthetic proteins remains largely unknown. Herein, we report positively charged iron oxide (Fe3O4) nanoparticles experience transformations in Arabidopsis thaliana plants in vivo that alter the formation and function of Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) protein corona, a key enzyme in the global carbon cycle. Elucidating rules of how nanoparticle properties and their transformations affect photosynthetic coronas will lead to more sustainable nanotechnology approaches for agriculture and the environment.