The major challenges of improving food security and biodiversity conservation are intricately linked. To date, the intersection of food security and biodiversity conservation has been viewed primarily through an agricultural “production lens”—for example, via the land sparing/sharing framework, or the concept of sustainable intensification. However, a productionist perspective has been criticized for being too narrow, and failing to consider other relevant factors, including policy, equity, and diversity. We propose an approach that conceptualizes rural landscapes as social–ecological systems embedded within intersecting multi-scalar processes. Based on such a framing, empirical research can be more clearly set in the context of system properties that may influence food security, biodiversity conservation, or both. We illustrate our approach through a description of contrasting agricultural systems within Brazil’s Cerrado region. We emphasize the need for new empirical research involving systematic comparisons of social–ecological system properties in landscapes threatened by food insecurity and ecosystem degradation.