Allogeneic hematopoietic stem cell transplantation (alloHSCT) is a common therapy for pediatric hematologic malignancies. With improved supportive care, addressing treatment‐related late effects is at the forefront of survivor long‐term health and quality of life. We previously demonstrated that alloHSCT survivors had increased adiposity, decreased lean mass, and lower bone density and strength, 7 years (median) from alloHSCT compared to their healthy peers. Yet it is unknown whether these deficits persist. Our longitudinal study characterized changes in muscle and bone over a period of 3.4 (range, 2.0 to 4.9) years in 47 childhood alloHSCT survivors, age 5–26 years at baseline (34% female). Tibia cortical bone geometry and volumetric density and lower leg muscle cross‐sectional area (MCSA) were assessed via peripheral quantitative computed tomography (pQCT). Anthropometric and pQCT measurements were converted to age, sex, and ancestry‐specific standard deviation scores, adjusted for leg length. Muscle‐specific force was assessed as strength relative to MCSA adjusted for leg length (strength Z‐score). Measurements were compared to a healthy reference cohort (n = 921), age 5–30 years (52% female). At baseline and follow‐up, alloHSCT survivors demonstrated lower height Z‐scores, weight Z‐scores, and leg length Z‐scores compared to the healthy reference cohort. Deficits in MCSA, trabecular volumetric bone density, and cortical bone size and estimated strength (section modulus) were evident in survivors (all p < 0.05). Between the two study time points, anthropometric, muscle, and bone Z‐scores did not change significantly in alloHSCT survivors. Approximately 15% and 17% of alloHSCT survivors had MCSA and section modulus Z‐score < −2.0, at baseline and follow‐up, respectively. Furthermore, those with a history of total body irradiation compared to those without demonstrated lower MCSA at follow‐up. The persistent muscle and bone deficits in pediatric alloHSCT survivors support the need for strategies to improve bone and muscle health in this at‐risk population. © 2022 American Society for Bone and Mineral Research (ASBMR).