The controlled filling of the pores of highly ordered mesoporous antiferromagnetic Co3O4 replicas with ferrimagnetic FexCo3-xO4 nanolayers is presented as a proof-of-concept toward the integration of nanosized units in highly ordered, heterostructured 3D architectures. Antiferromagnetic (AFM) Co3O4 mesostructures are obtained as negative replicas of KIT-6 silica templates, which are subsequently coated with ferrimagnetic (FiM) FexCo3-xO4 nanolayers. The tuneable magnetic properties, with a large exchange bias and coercivity, arising from the FiM/AFM interface coupling, confirm the microstructure of this novel two-phase core-shell mesoporous material. The present work demonstrates that ordered functional mesoporous 3D-materials can be successfully infiltrated with other compounds exhibiting additional functionalities yielding highly tuneable, versatile, non-siliceous based nanocomposites.