Campomanesia pubescens (gabiroba) is a fruit tree that is native to the Cerrado and that has commercial potential and medicinal properties. It has recalcitrant seeds that do not tolerate desiccation and storage. Here, C. pubescens plants were grown in vitro under different light qualities. Light-emitting diodes (LEDs) were used at wavelengths for white (W) and blue in combination with red in the proportions BR (1:1), BR (1:3) and BR (3:1), at 100 ± 5 μmol m-2 s-1 over a 16-hour photoperiod. The leaf anatomy, chlorophyll a fluorescence, chloroplast pigments and malondialdehyde (MDA) content were evaluated. Studies on Cerrado plants grown in vitro focusing on light quality and its effects on plant development and growth are scarce. Records of anatomical and physiological C. pubescens characteristics when grown in vitro under different lighting qualities using LEDs are nonexistent. In this context, the aim of this study was to analyze the anatomical and physiological responses of C. pubescens seedlings from in vitro cultivation under different light qualities, to support future studies on the propagation and conservation of this species. This work is a pioneer for this species. When the plants were cultivated in combinations of blue/red LEDs 1:1 and 3:1, they yielded higher biomass, presenting higher epidermis and chlorenchyma values with greater stomatal density and functionality, better photosynthetic efficiency, higher Y(II) values, qP and higher total chlorophyll concentrations, and thus these lights did not cause oxidative damage compared to the white (control) LEDs. This study contributed to a better understanding of the anatomical and physiological changes in C. pubescens plants grown in vitro under different light qualities. C. pubescens plants exhibited varied anatomical and physiological characteristics depending on the spectrum of light used here. The combinations of BR (1:1) or BR (3:1) LEDs are promising for the propagation of the species, given their positive influence on most of the studied traits.