Magnetic cobalt ferrite/silica microparticles having both an original morphology and an anisotropic nanostructure are synthesized through the use of an external magnetic field and nanoparticles characterized by a high magnetic anisotropy. The association of these two factors implies that the ESE (emulsion and solvent evaporation) sol-gel method employed here allows the preparation of silica microellipsoids containing magnetic nanoparticles aggregated in large chains. It is clearly shown that without this combination, microspheres characterized by an isotropic distribution of the magnetic nanoparticles are obtained. While the chaining of the cobalt ferrite nanoparticles inside the silica matrix is related to the increase of their magnetic dipolar interactions, the ellipsoidal shape of the microparticles may be explained by the elongation of the sol droplets in the direction of the external magnetic field during the synthesis. Because of their highly anisotropic structure, these microparticles exhibit permanent magnetic moments, which are responsible, at a larger scale, for the existence of strong magnetic dipolar interactions. Therefore, when they are dispersed in water, the microellipsoids self-assemble into large and irregular chains. These interactions can be reinforced by the use of external magnetic field, allowing the preparation of very large permanent chains. This research illustrates how nanostructured particles exhibiting complex architectures can be elaborated through simple, fast, and low-cost methods, such as the use of external fields in combination with soft chemistry.