Transitional metal oxides are promising anode materials for sodium ion batteries (SIBs) due to their high theoretical capacities and material abundance; however, their sodium storage capability is significantly hindered by the sluggish sodiation/desodiation reaction kinetics. Herein, towards achieving fast and durable sodiation/desodiation reaction, Fe3O4 and Co3O4 nanocrystals encapsulated in carbon micro-spheres are synthesized via a biochemistry approach using recombinant elastin-like polypeptides containing hexahistidine tag (ELP16-His) followed by annealing. Fe3O4 and Co3O4 nanocrystals of approximately 5 nm in size, which are uniformly dispersed in a carbon matrix, are obtained. The carbon-encapsulated metal oxides exhibit encouraging sodium storage capacities (657 and 246 mA h g−1 at 0.1 and 2 A g−1, respectively, for carbon-encapsulated Fe3O4; 583 and 183 mA h g−1 at 0.1 and 2 A g−1, respectively, for carbon-encapsulated Co3O4), and have a high capacity retention after 100 cycles at 0.5 A g−1. The superior electrochemical properties of the carbon-encapsulated metal oxide nanocrystals demonstrate their potential for use as anode materials for high-capacity, high-rate and durable sodium storage.