Background Intersectoral actions (ISA) are a recognized relationship between the health sector and other sectors to improve health outcomes. Although a frequent topic in public health, evidence for systematic evaluation of implementation of ISA is scarce. An intersectoral health intervention for infants under one-year-old with, and at risk of, stunting (low height-for-age) was developed by a public-private partnership in Bogotá, Colombia, during 2018 and 2019. Here we report a case study conducted in parallel to the intervention designed to assess factors that influenced implementation of the ISA. Methods The case study was developed using a concurrent mixed-methods design, with the qualitative component giving context to the quantitative results. The qualitative component was obtained from four workshops, three focal groups, and 17 semi-structured interviews with actors involved in the intersectoral intervention. The quantitative component was obtained with two questionnaires that evaluated perceptions on improvement and partnership functioning of the ISA. Results This study collected information from 122 participants. The intervention demanded intersectoral collaboration. Political will, motivated human resources, and recognition that health results from collaboration facilitated intersectoral actions. Intersectoral actions were limited by difficulties in engaging the health sector, communication challenges related to local health service decentralization, and administrative barriers. Conclusions Intersectoral actions have been recently discussed in the literature due to challenges on implementation, idealization, inconsistent demands, and doubts about economic outcomes. The implementation of intersectoral public health interventions can be jeopardized by a lack of coordination and management skills.