Mesoporous Silica Nanoparticles (MSN) are used in an increasing number of applications in nanomedicine. Their synthesis and external/internal functionalization have been extensively studied as well as their biological properties. Nevertheless, the conventional drug loading processes of MSN (such as impregnation), do not enable sufficient efficiency and are difficult to consider on an industrial scale. To overcome these limitations, we implemented an innovative co-spray-drying process, using a nano spray-dryer, to load MSN with ibuprofen molecules. In this contribution, complementary techniques were used to perform a multi-scale characterization of the loaded particles. Spray-dried powders have been analysed from aggregates size and morphology to pore loading and ibuprofen conformation. This study demonstrates that ibuprofen/silica weight ratio in the initial suspension strongly affects the location (into 2 mesopores or external) and the conformation (crystallized, amorphous or liquid-like) of ibuprofen. The quantification of each phase has allowed calculating precise loading rates and demonstrate tunable pore filling.