Abstract Background Integrated Management of Childhood Illnesses (IMCI) is a strategy developed by the World Health Organization (WHO) and UNICEF in 1992. It was deployed as an integrated approach to improve children’s health in the world. This strategy is divided into three components: organizational, clinical, and communitarian. If the Integrated Management of Childhood Illnesses implementation-related factors in low- and middle-income countries are known, the likelihood of decreasing infant morbidity and mortality rates could be increased. This work aimed to identify, from the clinical component of the strategy, the implementation-related factors to Integrated Management of Childhood Illnesses at 18 Colombian cities. Methods A quantitative cross-sectional study was performed with a secondary analysis of databases of a study conducted in Colombia by the Public Health group of Universidad de Los Andes in 2016. An Integrated Care Index was calculated as a dependent variable and descriptive bivariate and multivariate analyses to find the relationship between this index and the relevant variables from literature. Results Information was obtained from 165 medical appointments made by nurses, general practitioners, and pediatricians. Health access is given mainly in the urban area, in the first level care and outpatient context. Essential medicines availability, necessary supplies, second-level care, medical appointment periods longer than 30 min, and care to the child under 30 months are often related to higher rates of Integrated Care Index. Conclusion Health care provided to children under five remains incomplete because it does not present the basic minimums for the adequate IMCI’s implementation in the country. It is necessary to provide integrated care that provides medicine availability and essential supplies that reduce access barriers and improve the system’s fragmentation.