Plant reproductive failure is a critical concern for conserving rare and endangered species that typically have low‐density and sparse populations. One important factor contributing to reproductive failure is the spatial arrangement of plants within a population, which can lead to isolation and negatively affect seed production, particularly in obligate outcrossers. Additionally, plant size can compound this effect, influencing seed production via multiple processes. Here, we investigate how spatial distribution and size influence the reproductive success of Vasconcellea chilensis, an endemic‐threatened papaya species in Chile. We first examined whether V. chilensis can produce seeds via apomixis using pollinator exclusion experiments. We then used Spatial Point Pattern Analysis (SPPA) in three populations to explore the spatial arrangement of plants. Finally, we assessed whether plant size and neighbor distance influence the reproductive success V. chilensis is a dioecious shrub unable to produce fruits through apomixis. The SPPA revealed significant clustering of female and male plants at different spatial scales, indicating a non‐random distribution. Moreover, a significant spatial association between the sexes was observed. In two populations, closer proximity to male plants was linked to higher seed production. Our study revealed that the reproductive system of V. chilensis is susceptible to distance‐dependent reproductive failure due to pollen limitation. While the species' spatial structure may partially mitigate this risk, female plants isolated from male counterparts will likely experience reduced seed set.