Nowadays, the interest in the design of particles that combine therapy and diagnosis simultaneously to obtain a theranostic material has increased. One of the most used materials for MRI diagnosis is iron oxide, where clusters of superparamagnetic iron oxide (SPIONs) are noteworthy candidates. These particles are of high interest due to their broad range of applications, such as contrast agents, use in magnetic separation processes, and in hyperthermia therapy, among others. One of the major problems with their use is maintaining superparamagnetism while having the highest magnetization-to-particle ratio. In this work, microwave-assisted synthesis of clusters formed by SPIONs has been investigated. This synthesis strategy allows for significant reduction in the time and energy required to obtain SPION clusters. Also, the magnetization-to-particle ratio has been increased in comparison with single SPIONs. Subsequently, the clusters are coated with amorphous silica using the Stöber method, followed by mesoporous (MS) silica using the atrane method, which offers high and conformal coating homogeneity over the clusters. Surfactant extraction was done using a simple mixture of water, ethanol, and sodium chloride – avoiding the use of other organic solvents. Finally, as a proof of concept, the loading and release of a model molecule were studied to confirm that the SPION-NCs@MS presented in this work have great potential as theranostic agents.