Mutualistic interactions among organisms are fundamental to the origin and maintenance of biodiversity. Yet, the study of community dynamics often relies on values averaged at the species level, ignoring how intraspecific variation can affect those dynamics. We developed a theoretical approach to evaluate the extent to which variation within populations, in terms of interactions, can influence structural stability, a robust measure of species' likelihood of persistence in mutualistic systems. Next, we examine how intraspecific variation in mutualistic interactions affects species' persistence theoretically in a simplified community, which provides a solid foundation for contextualizing empirical results. This theoretical exploration revealed that differences in the benefits received by different individual types by mutualistic partners, as driven by the way interactions are distributed among those types due to individual specialization, strongly influence species persistence. Building on these insights, we move beyond the theoretical framework and work through an empirical case study involving three co-occurring plant species. Drawing from detailed field data on plant–pollinator interactions and plant fitness, we quantify intraspecific variation in the mutualistic benefits received by plants and incorporate this variation into estimations of structural stability. Through explicit consideration of this facet of intraspecific variation, we found that, for all three focal plant species, populations composed of individuals specialized in pollinator use promote the persistence of the plant species they belong to and their associated pollinator community, only in the absence of heterospecific plant competitors. However, more importantly, these positive effects do not hold when plant species compete with a broader, diverse plant community. In this case, two of the focal plant populations are more vulnerable when they comprise more specialized individuals and therefore are less likely to persist. By integrating the proposed theoretical approach with empirical data, this study highlights the importance of individual variation in promoting species persistence in mutualistic systems. In doing so, it not only advances our understanding of basic mechanisms that foster biodiversity maintenance but also provides practical insights for biodiversity conservation in the face of changing environmental conditions., Blanca Arroyo-Correa received funding from the Ministry of Universities of the Spanish Government (FPU19/02552 and EST23/00036) and a project grant from the Spanish Association of Terrestrial Ecology (AEET). Blanca Arroyo-Correa and Pedro Jordano were supported by grants CGL2017-82847-P and PID2022-136812NB-I00, funded by MCIN/AEI/10.13039/501100011033 and by the “European Union NextGenerationEU/PRTR”, grant P20-00736 from Junta de Andalucía, and a LifeWatch ERIC-SUMHAL project (LIFEWATCH-2019-09-CSIC-13), with FEDER-EU funding. E. Fernando Cagua acknowledges the support from the University of Canterbury Doctoral Scholarship, the Meadow Mushrooms Ltd.: University of Canterbury Postgraduate Scholarship, and a Education New Zealand: New Zealand Doctoral Research Scholarship. Daniel B. Stouffer acknowledges the support of a Rutherford Discovery Fellowship (RDF-13-UOC-003), administered by the Royal Society of New Zealand Te Apārangi., Peer reviewed