The Chinese government initiated one of the world's largest conservation programs involving agricultural ecosystems with the implementation of the ‘Grain for Green’ (Tui Geng Huan Lin) forest policy between 1999 and 2003. This is the first study to systematically quantify multiple dimensions of biodiversity, phytochemical quality and economic benefits associated with (1) the Grain for Green's tea (Camellia sinensis; Theaceae) initiative; (2) the state's previous forest policy involving tea populations in protected areas and; (3) the indigenous tea agro-ecosystems replaced or overlooked by this conservation program. There are several novel and unexpected findings. While forest populations contained the greatest ecological diversity, agro-forests and mixed crop plots were associated with the greatest genetic diversity, phytochemical quality and economic benefits. Indigenous management practices should be incorporated into conservation in China in order to create policies that are more aligned towards biodiversity conservation and sustainable livelihoods while allowing local communities to maintain their cultural identity through agrarian practices.