Kidney development is an extraordinary process involving many cell types orchestrating a proliferation, differentiation, and migratory journey into a fully functioning adult organ. Maternal nutrition has a major influence on the development of the embryo, and the kidney is no exception. A reduction in dietary protein intake by a pregnant mouse affects the growing kidney and the adult organ by reducing the number of nephrons in the offspring, but how this happens at the level of tissue development is only now being revealed. The nephrons are assembled through a tightly controlled cellular commitment and differentiation process. This study describes an intricate quantified 3D imaging and single cell sequencing approach to unravel the process by which kidney development is impacted by maternal nutrition. Using this approach, we discovered that the loss of the nephrons is brought about by a reduction in the number of early nephron progenitor rudiments via reductions in cellular proliferation, decreased cellular metabolism, and disruption of nephron progenitor cell commitment at the earliest stages of nephrogenesis.