Cocoa is an important crop in Colombia and a key productive alternative in post-conflict rural areas. Similar to other tropical production systems, yields are constrained by diseases such as black pod disease and frosty pod rot. This study evaluated the temporal and spatial epidemiological patterns of both diseases on three cocoa farms located in the Tequendama region of Colombia through analyses of disease incidence, severity, disease progress, and spatial distribution. Pod assessments were conducted over a six-month period, recording disease incidence, severity, pod developmental stage, and canopy stratum. Temporal analyses evaluated the effects of temperature and relative humidity on disease incidence, whereas spatial analyses examined disease distribution among farms and canopy strata and assessed horizontal spatial autocorrelation using Moran’s I. The results revealed contrasting epidemiological patterns. Black pod incidence was not significantly associated with temperature or relative humidity and remained low throughout the study period. Incidence increased from the lower to the upper canopy layer, and most variability occurred among trees rather than among farms. In contrast, frosty pod rot showed significant negative associations with temperature and relative humidity and consistently there was a higher incidence in the upper canopy layer. Severity and AUDPC values were also greater for frosty pod rot than for black pod disease. Moran’s I analyses did not detect significant spatial autocorrelation at the farm scale. These findings demonstrated that black pod disease and frosty pod rot differed in their temporal dynamics and canopy distribution patterns despite affecting the same host organ. The results highlighted the importance of disease-specific epidemiological approaches and provided information relevant for improving disease monitoring and management in cocoa production systems.