The development of the stone and formation of peach (Prunus persica) fruit were explored in this work using a proteomic approach. Sixty-eight proteins with different expression patterns were identified in both the endocarp and mesocarp during early fruit development (from 28 to 59 days after flowering) and the majority were involved in primary or secondary metabolism. In contrast to most proteins associated with primary metabolism in the endocarp, whose expression is down-regulated, expression of pyruvate dehydrogenase (PDH) unexpectedly increased exponentially. Moreover, its expression pattern was linearly positively correlated with the exponentially growing lignin content (R = 0.940), which suggests that PDH may play a role in endocarp lignification. Our data also revealed different spatiotemporal expressions of enzymes involved in the lignin and flavonoid pathways that provided proteome-level evidence to support the hypothesis that these two pathways are competitive during endocarp development. In addition, we observed endocarp-specific oxidative stress and propose that it may act as a stimulating factor in activating lignification and subsequent programmed cell death in the endocarp.