Roux-en Y gastric bypass (RYGB) surgery is an effective treatment for obesity;​ however, it may negatively impact skeletal health by increasing fracture risk. This increase may be the result not only of decreased bone mineral density but also of changes in bone microstructure, for example, increased cortical porosity. Increased tibial and radial cortical porosity of patients undergoing RYGB surgery has been observed as early as 6 months postoperatively;​ however, local microstructural changes and associated biological mechanisms driving this increase remain unclear. To provide insight, we studied the spatial distribution of cortical porosity in 42 women and men (aged 46 ± 12 years) after RYGB surgery. Distal tibias and radii were evaluated with high-resolution peripheral quantitative computed tomography (HR-pQCT) preoperatively and at 12 months postoperatively. Laminar analysis was used to determine cortical pore number and size within the endosteal, midcortical, and periosteal layers of the cortex. Paired t tests were used to compare baseline versus follow-up porosity parameters in each layer. Mixed models were used to compare longitudinal changes in laminar analysis outcomes between layers. We found that the midcortical (0.927 ± 0.607 mm⁻² to 1.069 ± 0.654 mm⁻², p = 0.004;​ 0.439 ± 0.293 mm⁻² to 0.509 ± 0.343 mm⁻², p = 0.03) and periosteal (0.642 ± 0.412 mm⁻² to 0.843 ± 0.452 mm⁻², p < 0.0001;​ 0.171 ± 0.101 mm⁻² to 0.230 ± 0.160 mm⁻², p = 0.003) layers underwent the greatest increases in porosity over the 12-month period at the distal tibia and radius, respectively. The endosteal layer, which had the greatest porosity at baseline, did not undergo significant porosity increase over the same period (1.234 ± 0.402 mm⁻² to 1.259 ± 0.413 mm⁻², p = 0.49;​ 0.584 ± 0.290 mm⁻² to 0.620 ± 0.299 mm⁻², p = 0.35) at the distal tibia and radius, respectively. An alternative baseline-mapping approach for endosteal boundary definition confirmed that cortical bone loss was not primarily endosteal. These findings indicate that increases in cortical porosity happen in regions distant from the endosteal surface, suggesting that the underlying mechanism driving the increase in cortical porosity is not merely endosteal trabecularization.