This work reports on an in-depth characterization of the nano- and microstructure of extruded starch foams loaded with the microalga Spirulina (1, 5 and 10 wt%), as well as the implications of Spirulina incorporation on the textural properties of the foams. Due to the gelatinization process occurring during extrusion, the crystalline and lamellar structures originally present in the starch granule were disrupted, resulting in very amorphous foams. Moreover, the crystalline structure of the fatty acids present in the raw microalga was lost during processing. The presence of Spirulina intracellular components induced the formation of more thermally-stable V-type crystallites through complexation with amylose, hence producing slightly more crystalline foams (XC∼5–9%) than the pure extruded starch (XC ∼3%). This affected the microstructure of the hybrid foams, which showed more densely packed and well-connected porous structures. Microstructural changes had an impact on the texture of the foams, which became harder with greater Spirulina loadings. The foams underwent very limited re-crystallization upon storage, which was further reduced by the presence of Spirulina. Interestingly, the free fatty acids from Spirulina re-crystallized and the resistant starch content in the 10% Spirulina foam increased, which could potentially be interesting from a nutritional perspective. These results show the potential of extrusion cooking to produce healthier snack foods and highlight the suitability of advanced characterization tools such as neutron tomography and small angle X-ray scattering to investigate food structure.