Agricultural practices of smallholder farming systems of Latin America can play an important role in reducing their exposure to the risks associated with climate extremes. To date, however, there is no systematic analysis of scientific evidence for the extent to which these practices can provide the multiple benefits needed for smallholders to adapt to climate extremes. In this paper, we searched scientific databases to review scientific evidence of the benefit provided by twenty-six practices in crops commonly farmed by smallholders in the region and highly relevant for their food and nutrition security; namely, coffee, maize and beans. We reviewed scientific documents (n = 304) published in the period 1953–2021 to register evidence of the practices’ effects on fifty-five benefits. Our analysis of these documents found measurement records (n = 924) largely based on field experiments (85%). Our results show strong evidence of the multiple benefits that some ecosystem-based practices (e.g., tree-based practices for coffee and no tillage for maize) can provide to support the adaptation to climate extremes of smallholder farming systems and enhance a farm’s natural assets (e.g., biodiversity, water, soil). We also found that the majority of research on practices in the region focused more on the socioeconomic dimension (54%) rather than on the capacity of practices to improve the natural assets of a smallholder farmers or reduce the impact of climate extremes. Given these knowledge gaps, we discuss the importance of a renovated investment in research to address existing knowledge gaps. Our concluding suggestions for future research include the need for systematizing existing knowledge from different sources (e.g., peer-reviewed, gray literature, farmers, extension agencies, etc.), and to assess the extent to which these practices can provide multiple benefits for smallholder farming systems by improving their wellbeing, reducing their vulnerability to different hydroclimatic extremes while also contributing to ecosystem services provision at the landscape level.