This paper focuses on an integrative “bricks-and-mortar” approach involving bioactive glass nanoparticles (bricks) covalently functionalized with a customized polymer (mortar) combined with the freeze-casting process. With the aim of obtaining a macroporous composite for bone substitution, composed of a spatially homogeneous assembly of nanoscale objects, we establish a method for the systematic elaboration of nanocomposite scaffolds. It was implemented through several steps from the synthesis of functionalized poly(d,l-lactide) (PDLLA) and SiO2–CaO binary bioactive glass nanoparticles (diameter around 164 nm) to the unidirectional freeze-casting process. The different stages include the first description of controlled PDLLA (Mn 8400 g·mol–1) grafting onto bioactive glass nanoparticle surfaces, their fine characterization and grafting quantification, and their mixing with free PDLLA chains (83 400 g·mol–1) during suspension formulation. This paper emphasizes the effect of the working temperature during the freeze-casting process on the multiscale spatial organization of resulting scaffolds such as the porosity morphology (lamellar and tubular), size (from 30 to 380 μm), anisotropy, and orientation. In addition to porosity, our results demonstrate a rosary-like organization of PDLLA-grafted nanoparticles in pore walls. The higher homogeneity in the spatial distribution of grafted nanoparticles over the height of scaffolds and at a micron scale confirms the validity of the “bricks-and-mortar” concept to prevent or limit aggregation. In particular, this study highlights the correlation between nanoparticle functionalization and mechanical properties, especially the recovery rate after compression tests. These results lay the foundation for the development of tunable materials for bone substitution, via potential enhancement of bioactivity and cell colonization.