<p>Cultivating threatened plant species is vital for conservation, safeguarding against extinction by ensuring propagation and maintaining genetic diversity. Here, we conducted an integrative morphological, physiological, and quantitative proteomic analysis of <i>Stephanopodium engleri</i> plants grown under different substrates and nutritional sources. <i>Stephanopodium engleri</i> is a threatened tree endemic to the Iron Quadrangle, a Brazilian mining region. Different nutritional sources resulted in changes in the growth of <i>S. engleri</i>, with N, P, and micronutrients identified as the most limiting nutrients. The species exhibited maximum growth with half of the applied fertilization, suggesting a low nutritional requirement. The highest growth was related to adjustments in the photosynthetic apparatus and protein regulation, with no significant differences in morpho-anatomical traits. The most representative proteins displayed a diverse array of metabolic functions, particularly related to iron and zinc homeostasis, photosynthesis and energy pathways and reactive oxygen species signaling. Plants with lower carbon assimilation and growth exhibited down-regulation of these proteins. Our findings provide valuable insights into <i>S</i>. <i>engleri</i> physiology and adaptations, emphasizing the importance of minimum fertilization to produce high-quality seedlings. These results also support broader conservation efforts aimed at preventing the species from becoming extinct, including reinforcing natural populations, establishing new ones, and supporting the maintenance of germplasm banks and living collections.</p>