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As smallholders in the global South engage in new ways with agricultural markets, they change their farming strategies and use of agricultural inputs. In many locales, heavy use of synthetic fertilizers and pesticides has caused state authorities figurative headaches and farmers actual health hazards and soil degradation. Structural forces and simplistic views of farmers impede creating soil management regimes that build human capabilities and enrich landscapes. It has been argued that agricultural commercialization and urbanization generate metabolic rifts—gaps in nutrient cycling that impoverish soils and accumulate wastes. Replacement of organic with synthetic inputs is central to this dynamic. We join metabolic rift theory with livelihood analysis to examine how varying livelihood strategies differentiate input use in an area of southwest China where farming is partially commercialized. We draw on household survey, focus group, and interview data to identify five household clusters with distinct on-farm activity patterns. Regression analyses show that these farming strategies mediate effects of household and community attributes on use of synthetic fertilizers, synthetic pesticides, and organic manure fertilizer. Strategies associated with diverse on-farm crop rotations are associated with greater use of manure. Emergent tree-borne crops are associated with greater pesticide use, but new high-elevation cash crops are linked to less use of both synthetic and organic inputs. These variations have gendered impacts: women’s work around compost fertilizer gives way to male-dominated synthetic input management. Digging into the practices that underlie these variations, we demonstrate the uneven processes through which metabolic rifts tear open and the necessity for soil enhancement efforts to address farmers’ variegated practices.