Honey is highly appreciated for its functional properties, however its consume is restricted for children under one year old due to the potential presence of Clostridium botulinum spores, which could cause botulism. Within this context the thermal treatment of tyndallization could become in an alternative to treat honey with the aim of eliminating Clostridium botulinum spores. The objective of this study was to apply thermal treatments (pasteurization and tyndallization) to Apis mellifera and Tetragonisca angustula honeys, to evaluate the effect on some physicochemical and microbiological parameters associated to honey quality. The honey bottled in amber glass recipients was pasteurized to 65 °C for 15 and 21 min and was tyndallized to 80 °C during five and seven minutes. The tyndallized samples were immediately removed from the thermostatic bath and cooled then, were incubated at 37 °C under anaerobic conditions for 72 h, this cycle was repeated two times more, and after that the samples were analyzed. Harmonized methods of the International Honey Commission were used for physicochemical analyses, while methods from the International Commission on Microbiological Specifications for Foods (ICMSF) were used for microbiological tests. Honey samples heat treated for pasteurization and tyndallization during 15 and 21 min showed statistically significant differences (p< 0.05), in terms of moisture and diastase activity, in comparison to untreated honey, although their values were within the limits established by the Colombian regulations, except T. angustula moisture. Hydroxymethylfurfural (HMF) raised in A. mellifera honey pasteurized and color raised in tyndallized honeys. Mesophilic bacteria, molds and yeasts levels of T. angustula honey were not within the limits established by the Colombian regulations. Mesophilic bacteria, molds and yeasts and total coliforms levels decreased in T. angustula honey heat treated. While sulfite-reducers anaerobic spores increased in T. angustula honey pasteurized and Clostridium perfringens increased in T. angustula tyndallized honey.