Background <p>Breastfeeding is generally associated with favorable neurodevelopmental outcomes, but toddlers who continue receiving breast milk may remain at risk of micronutrient inadequacy when complementary feeding is insufficient. This study examined associations among breastfeeding status at assessment, micronutrient biomarkers, thyroid function, and Bayley-III developmental outcomes in Taiwanese toddlers.</p> Methods <p>This cross-sectional study was conducted at Shin Kong Wu Ho-Su Memorial Hospital, Taipei, Taiwan, between February 2019 and December 2020. Among 577 eligible toddlers aged 12–24 months screened during routine vaccination visits, 112 completed the study protocol. After excluding two toddlers with abnormal thyroid-stimulating hormone concentrations, 110 were included in the final analysis. Breastfeeding status was classified as breastfeeding at assessment (BFA; receiving any breast milk, <i>n</i> = 27) or not breastfeeding at assessment (NBFA; no longer receiving breast milk, <i>n</i> = 83). Laboratory measures included hemoglobin, ferritin, serum 25-hydroxyvitamin D₃, urinary iodine concentration, thyroid-stimulating hormone, free triiodothyronine, and free thyroxine. Neurodevelopment was assessed using the Bayley Scales of Infant and Toddler Development, Third Edition. Associations between breastfeeding status and developmental scores were examined using hierarchical multivariable linear regression.</p> Results <p>Toddlers in the BFA group had lower ferritin concentrations than those in the NBFA group and a higher frequency of iron deficiency (6/27, 22.22% vs. 4/83, 4.82%). Vitamin D insufficiency was common overall and did not differ clearly between groups. Thyroid profiles were within age-appropriate reference ranges; however, free thyroxine was higher in the BFA group than in the NBFA group. In unadjusted linear regression, BFA was associated with higher cognitive scores (unstandardized regression coefficient [B] = 4.95, 95% CI 0.06 to 9.83) and language scores (B = 6.94, 95% CI 0.77 to 13.11), but not motor scores (B = 2.37, 95% CI -1.35 to 6.09). After adjustment for child age, sex, maternal age, and maternal education, the associations remained for cognition (B = 5.21, 95% CI 0.27 to 10.16) and language (B = 7.13, 95% CI 1.25 to 13.01). Free thyroxine was positively associated with Bayley-III cognitive, language, and motor composite scores.</p> Conclusion <p>Among Taiwanese toddlers aged 12–24 months, breastfeeding at assessment was associated with lower ferritin concentrations, a higher frequency of iron deficiency, and higher cognitive and language Bayley-III composite scores after adjustment for child and maternal characteristics. Free thyroxine may represent a potential biological pathway linking breastfeeding status with early developmental outcomes, although larger longitudinal studies are needed.</p>