Context Kikuyu grass (Cenchrus clandestinus (Hochst. ex Chiov.) Morrone) is native to the Central African highlands and was introduced to Colombia in 1928 to feed animals. Despite its low genetic diversity and proven genetic clonality, this species has shown broad phenotypic variation and has become the primary forage resource for livestock production systems in the Colombian highlands. However, it is necessary to determine whether genetic diversity should be considered when designing management programs. Aims We aimed to determine which variables among location, altitude and population genetic structure explain the phenotypic variation of Kikuyu grass samples across livestock farms at high altitudes. Methods We used principal component analysis, redundancy analysis and partial redundancy analysis to understand the contribution of three explanatory variables (three high-altitude ranges, six locations and two or five genetic clusters) and 30 covariables (pasture management and soil traits of each farm) to explain 18 phenotypic variables of 146 Kikuyu grass samples from high-altitude livestock farms in Colombia. Key results All explanatory variables and covariables explained 39.1–41.5% of the phenotypic variation of Kikuyu grass in Colombia. However, the effect of the genetic structure based on two or five clusters was negligible. By comparison, locality, altitude and 13 covariables of productive system management and soil traits were significant. Conclusions Genetic population structure was insignificant in explaining the phenotypic variation of Kikuyu grass in Colombia. Implications Future research on Kikuyu grass in Colombia should focus on farm management variables and soil trait analyses.