A study related to the physicochemical composition and profile of phenolic compounds and flavonoids was performed on honey of Apis mellifera L. (Hymenoptera: Apidae) obtained in coffee-growing areas from Sierra Nevada de Santa Marta, in Colombia. A total of 67 samples were obtained from hives installed on coffee farms classified according to their type of production: organic or conventional. The results of physical properties and chemical composition analyses showed that the honey samples were within the limits established by international regulations. The phenolic compounds and flavonoids identified as chemical markers of interest were coumaric, caffeic, and cinnamic acid, as well as luteolin, quercetin, and isorhamnetin. Tukey's multiple comparison tests showed no major significant differences between the composition of the honey samples from organic coffee growing areas compared to conventional plantations, mainly because of the similarity of floral sources in the surrounding area. Additionally, an analysis of pesticides and heavy metals showed the absence of such components in all samples, confirming that regardless of the type of production, this region is an environmentally clean agricultural zone. This information will generate bases for the differentiation by origin of honey from Sierra Nevada de Santa Marta, aimed to improve their marketing and promote added value.