In vitro cultivation of Melaleuca could contribute to the cloning of superior genotypes. Studies of factors affecting micropropagation are needed, such as the interaction with light-emitting diodes (LEDs) and plant growth regulators added to the culture media. This study aimed at better understanding the effects of spectra on the development and physiology of melaleuca cultivated in vitro, as well as the interaction of LEDs with the main cytokinin used in micropropagation, N6-Benzylaminopurine (6-BAP). 6-BAP, spectra, and their interaction had a significant effect on most of the variables analyzed, altering the in vitro development and chlorophyll concentrations in the plants, as well as changing different variables in the culture medium, such as pH, EC, and levels of Ca2+, Mg2+, and P, and nutrient accumulation in the shoots. The results demonstrate that the main effects of adding BAP to the in vitro cultivation of melaleuca are an increase in the number of shoots, which resulted in greater fresh and dry masses; a reduction in height and chlorophyll content; complete inhibition of adventitious rooting; higher consumption of Mg, and lower consumption of Ca and P from the culture medium; higher content of Fe, and lower content of P, S, Mn, Cu and B in the in vitro shoot tissues.