The projected impact of climate change on agro-ecological systems is considered widespread and significant, particularly across the global tropics. As in many other countries, adaptation to climate change is likely to be an important challenge for Colombian agricultural systems. In a recent study, a national-level assessment of the likely future impacts of climate change on agriculture was performed (Ramirez-Villegas et al. Clim Chang 115:611–628, 2012, RV2012). The study diagnosed key challenges directly affecting major crops and regions within the Colombian agricultural system and suggested a number of actions thought to facilitate adaptation, while refraining from proposing specific strategies at local scales. Further insights on the study were published by Feola (2013) (F2013), who stressed the need for transformative adaptation processes to reduce vulnerability particularly of resource-limited farmers, and the benefits of a predominantly stakeholder-led approach to adaptation. We clarify that the recommendations outlined in RV2012 were not intended as a recipe for multi-scale adaptation, but rather a set of actions that are required to diagnose and develop adaptation actions particularly at governmental levels in coordination with national and international adaptation initiatives. Such adaptation actions ought to be, ideally, a product of inclusive sub-sectorial assessments, which can take different forms. We argue that Colombian agriculture as a whole would benefit from a better outlining of adaptation needs across temporal scales in sub-sectorial assessments that take into account both RV2012 and F2013 orientations to adaptation. We conclude with two case studies of research on climate change impacts and adaptation developed in Colombia that serve as examples of realistic, productive sectorial and sub-national assessments.