Agricultural systems in sub-Saharan Africa face mounting climate variability, yet the causal mechanisms linking biodiversity-based adaptation practices to yield stability remain poorly identified. Rather than reporting empirical results, the analysis establishes the theoretical and methodological foundations for causal inference in this context, addressing the central identification challenge that farmers self-select into adaptation practices based on unobserved characteristics correlated with outcomes. The proposed design exploits temporal variation in the staggered adoption of conservation practices across spatially distinct farming communities, combined with a composite spatial index of biophysical vulnerability constructed from slope, drainage density, rainfall intensity, land cover, soil permeability, elevation, and distance to channels. The article articulates the causal model linking biodiversity-mediated ecosystem services to yield stability, specifies the identifying assumptions required for valid estimation, and develops a geographic information systems workflow for constructing treatment and comparison groups. The contribution is a replicable analytical template that aligns ecological theory with econometric identification, enabling future empirical work to move beyond associational claims about conservation agriculture in East Africa.