The objective of this study was to evaluate whether there are negative effects of the partial replacement of white corn with rye along with xylanase supplementation on overall bone quality, eggshell mineralization, and mechanical strength in laying hens. From the 26th week of life, ISA Brown laying hens were fed either a wheat–corn diet or a diet containing 25% rye, with or without xylanase. The experimental period lasted for 25 weeks, until birds reached their 50th week of age, after which bone and eggshell quality indices were assessed. Eggshell thickness and eggshell Ca content of eggs from rye-fed hens were improved by xylanase supplementation. No differences in the mechanical properties of the eggshells were observed between treatments, except for the diet-dependent changes in egg deformation. Rye inclusion had no effect on the mechanical properties of bone. Xylanase supplementation, irrespective of the diet, had a positive effect on bone strength and increased tibia Ca content, as well as the content of several microelements. Hence, hybrid rye combined with wheat can replace 25% of corn in layer diets without compromising shell quality or bone mineral content. Xylanase supplementation in these diets is recommended since its inclusion improves both bone strength and quality.