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Abstract There has been a growing interest in the seed microbiome due to its important role as an end and starting point of plant microbiome assembly that can have consequences for plant health. However, the effect of abiotic conditions on the seed microbial community remains unknown. We performed a pilot study in a controlled growth chamber to investigate how the endophytic seed microbiome of the common bean (Phaseolus vulgaris L. (var. Red Hawk)) was altered under abiotic treatments relevant for crop management with changing climate. Bean plants were subjected to one of three treatments: 66% water withholding to simulate mild drought, 50% Hoagland nutrient solution to simulate fertilization, or control with sufficient water and baseline nutrition. We performed 16S rRNA gene amplicon sequencing and ITS1 amplicon sequencing of the endophytic DNA to assess seed bacterial/archaeal and fungal community structure, respectively. We found that variability in the seed microbiome structure was high while alpha diversity was low, with tens of taxa present. Water withholding and nutrient addition altered the seed microbiome structure for bacterial/archaeal communities as compared to the control, and each treatment resulted in a distinct microbiome structure. There were no statistically supported differences in the fungal microbiome across treatments. While we discuss several limitations of this study, the promising results suggest that further investigation is needed to better understand abiotic or stress-induced changes in the seed microbiome, the mechanisms that drive those changes, and their implications for the health and stress responses of the next plant generation. Importance Seed microbiome members initiate the assembly of plant-associated microbial communities, but the environmental drivers of endophytic seed microbiome composition are unclear. Here, we exposed plants to short-term drought and fertilizer treatments during early vegetative growth and quantified the microbiome composition of the seeds that were ultimately produced. We found that seeds produced by plants stressed by water limitation or receiving nutrient addition had statistically different endophytic bacterial/archaeal microbiome compositions from each other and from seeds produced by control plants. This work suggests that the abiotic experience of a parental plant can influence the composition of its seed microbiome, with unknown consequences for the next plant generation.