Despite various hypothesized benefits of dietary isoflavone genistein (GEN) from soy-based products, many questions surrounding GEN's immunotoxic effects, especially during perinatal exposure, have yet to be answered. The objective of the study was to determine if there existed a sex-specific effect of GEN on type 1 diabetes (T1D) following perinatal exposure. We exposed offspring of non-obese diabetic (NOD) mice to GEN per oral at a physiological dose (20 mg/kg body weight) from embryonic day 7 to postnatal day (PND) 21. In female offspring, perinatal GEN dosing significantly increased the incidence of T1D at early time points, and the exacerbation was associated with decreased serum levels of interleukin (IL)-10, IgG2a, and IgM. In male offspring dosed with GEN, a decrease in serum IgG1 was also observed. Flow cytometric analysis in females suggested an increased pro-inflammatory splenic CD5+CD24- and CD4-CD8+ cell counts, while both %T cells and %CD4+ T cells were significantly decreased in males, suggesting an anti-inflammatory effect. Gut microbiota (GMB) analysis indicated that fecal microbiota from PND 90 female offspring exhibited an increased level of Enterobacteriales (suggesting a pro-inflammatory response), while the similar changes were not found in PND 30 females. Moreover, RNA sequencing showed that intestinal α-defensin expression was down-regulated in GEN-treated females, supporting a pro-inflammatory response. However, perinatal GEN administration perturbed GMB toward an anti-inflammatory response in PND 90 males. Taken together, a strong sex-specific effect was found in the perinatal GEN exposure window, and the T1D exacerbation in NOD females was associated with GMB-related immunomodulatory mechanisms.