Estrogen deficiency associated with menopause is accompanied by an increase in the rate of bone remodeling and the appearance of a remodeling imbalance; each of the greater number of remodeling transactions deposits less bone than was resorbed, resulting in microstructural deterioration. The newly deposited bone is also less completely mineralized than the older bone resorbed. We examined whether breastfeeding, an estrogen‐deficient state, compromises bone microstructure and matrix mineral density. Distal tibial and distal radial microarchitecture were quantified using high‐resolution peripheral quantitative computed tomography in 58 women before, during, and after breastfeeding and in 48 controls during follow‐up of 1 to 5 years. Five months of exclusive breastfeeding increased cortical porosity by 0.6% (95% confidence interval [CI] 0.3–0.9), reduced matrix mineralization density by 0.26% (95% CI 0.12–0.41) (both p < 0.01), reduced trabecular number by 0.22 per mm (95% CI 0.15–0.28), and increased trabecular separation by 0.07 mm (95% CI 0.05–0.08) (all p < 0.001). Relative to prebreastfeeding, at a median of 2.6 years (range 1 to 4.8) after cessation of breastfeeding, cortical porosity remained 0.58 SD (95% CI 0.48–0.68) higher, matrix mineralization density remained 1.28 SD (95% CI 1.07–1.49) lower, and trabeculae were 1.33 SD (95% CI 1.15–1.50) fewer and 1.06 SD (95% CI 0.91–1.22) more greatly separated (all p < 0.001). All deficits were greater than in controls. The results were similar at distal radius. Bone microstructure may be irreversibly deteriorated after cessation of breastfeeding at appendicular sites. Studies are needed to establish whether this deterioration compromises bone strength and increases fracture risk later in life. © 2016 American Society for Bone and Mineral Research.