Endospore formation is a starvation-induced developmental pathway in Bacillus subtilis involving an asymmetrically-positioned cell division event that generates two cells, the smaller forespore and the larger mother cell. We previously demonstrated that sporulation is accompanied by metabolic differentiation of these two cells, and the depletion of enzymes in central metabolism from the developing spore. This disables spore metabolism and makes the forespore dependent on mother cell metabolism to produce metabolic building blocks for the biosynthesis of proteins, RNA and phospholipids. The mdfA (yjbA) gene was identified as being required for metabolic differentiation and this data set compares the proteome of wild-type and mdfA spores to assess the impact of metabolic differentiation on metabolism.