Industrial agriculture (IA) has been recognized among the main drivers of biodiversity loss, climate change, and native pollinator decline. Here we summarize the known negative effects of IA on pollinator biodiversity and illustrate these problems by considering the case of Chile, a “world biodiversity hotspot” (WBH) where food exports account for a considerable share of the economy in this country. Most of Chile’s WBH area is currently being replaced by IA at a fast pace, threatening local biodiversity. We present an agroecological strategy for sustainable food production and pollinator conservation in food-producing WBHs. In this we recognize native pollinators as internal inputs that cannot be replaced by IA technological packages and support the development of agroecological and biodiversity restorative practices to protect biodiversity. We suggest four fundamental pillars for food production change based on: (1) sharing the land, restoring and protecting; (2) ecological intensification; (3) localized knowledge, research, and technological development; and (4) territorial planning and implementation of socio-agroecological policies. This approach does not need modification of native pollination services that sustain the world with food and basic subsistence goods, but a paradigm change where the interdependency of nature and human wellbeing must be recognized for ensuring the world’s food security and sovereignty.