Rubisco sustains the biosphere through the fixation of CO2 into biomass. In plants and cyanobacteria, Form I Rubisco is structurally comprised of large and small subunits, whereas all other Rubisco Forms lack small subunits. Thus, the rise of the Form I complex through the innovation of small subunits represents a key, yet poorly understood, transition in Rubisco’s evolution. Through metagenomic analyses, we discovered a previously uncharacterized clade sister to Form I Rubisco that evolved without small subunits. This clade diverged prior to the evolution of cyanobacteria and the origin of the small subunit; thus, it provides a unique reference point to advance our understanding of Form I Rubisco evolution. Structural and kinetic data presented here reveal how a proto-Form I Rubisco assembled and functioned without the structural stability imparted from small subunits. Our findings provide insight into a key evolutionary transition of the most abundant enzyme on Earth and the predominant entry point for nearly all global organic carbon.