Photothermal release of cargo molecules has been extensively studied for bioapplications. For instance, microcapsules decorated with plasmonic nanoparticles have been widely used in in vitro assays. However, some concerns about their suitability for some in vivo applications cannot be easily overcome, in particular the limited penetration depth of light (even infrared). Magnetic nanoparticles are alternative heat-mediators for local heating, which can be triggered by applying an alternating magnetic field (AMF). AMFs are much less absorbed by tissue than light and thus can penetrate deeper overcoming the above mentioned limitations. Here we present iron oxide nanocube-modified microcapsules as a platform for magnetically triggered molecular release. Layer-by-layer assembled polyelectrolyte microcapsules with 4.6 μm diameter, which had 18 nm diameter iron oxide nanocubes integrated in their walls, were synthesized. The microcapsules were further loaded with an organic fluorescent polymer (Cascade Blue-labelled dextran), which was used as a model of molecular cargo. Through an AMF the magnetic nanoparticles were able to heat their surroundings and destroy the microcapsule walls, leading to a final release of the embedded cargo to the surrounding solution. The cargo release was monitored in solution by measuring the increase in both absorbance and fluorescence signal after the exposure to an AMF. Our results demonstrate that magnetothermal release of the encapsulated material is possible using magnetic nanoparticles with a high heating performance.