<p><i>Tithonia diversifolia</i> (Hemsl.) A. Gray plays an important role in tropical agroforestry systems due to its ability to recycle phosphorus. Adapted to phosphorus-limited conditions, <i>T. diversifolia</i> has developed strategies to acquire this nutrient, including symbiotic relationships with mycorrhizal fungi that facilitate phosphorus mobilization. This occurs through rhizosphere acidification and the secretion of low-molecular-weight internal organic acids. However, research focuses on organic acids in isolation, overlooking the contributions of root characteristics, mycorrhizal abundance and hyphal growth. This study examined the content of low molecular weight internal organic acids, root characteristics, and mycorrhizal associations, and their role in phosphorus acquisition and impact on shoot biomass in three <i>T. diversifolia</i> genotypes. Differences (<i>p</i> &lt; 0.05) in internal organic acid content were observed in all <i>T. diversifolia</i> genotypes. In the Costa Rican genotype, succinic, malic, and fumaric acids in leaf tissue were associated (<i>p</i> &lt; 0.05) with root length and root length density, while in the Mexican genotype, citric and fumaric acids were linked (<i>p</i> &lt; 0.05) to the number of roots. Succinic and citric acids in root tips were associated (<i>p</i> &lt; 0.05) with the number of stems in the Indonesian genotype, while in the Costa Rican genotype, these acids were linked (<i>p</i> &lt; 0.05) to specific root length. The Mexican genotype had a higher specific root length density (<i>p</i> &lt; 0.05), likely allowing it to efficiently capture nutrients and better acclimate to a phosphorus limited environment. The Mexican genotype had a greater number of mycelial entry points (<i>p</i> &lt; 0.05) and mycelium length density (<i>p</i> &lt; 0.05) and allocated its shoot biomass to fewer but larger branches.</p>