In this work we present the concept of embedded volumetric entities for the isogeometric modeling and shape optimisation of multi-patch solids. Using NURBS composition, we can enforce a priori the geometric connection between patches while performing shape optimisation of a given patch composing the structure. While being geometrically compatible, the patches’ non-conforming meshes are coupled using a mortar method. The approach allows us to guarantee geometric connection of all patches even for large geometric changes through a gradient-based optimisation process. The efficiency of the method is demonstrated on the real model of an aircraft engine blade assembly.