Magnetic force microscopy (MFM) is an atomic force microscopy (AFM)-based technique to map magnetic domains in a sample. MFM is widely used to characterize magnetic recording media, magnetic domain walls in materials, nanoparticles and more recently iron deposits in biological samples. However, conventional MFM requires multiple scans of the samples, suffers from various artifacts and is limited in its capability for multimodal imaging or imaging in a fluid environment. We propose a new modality, namely indirect magnetic force microscopy (ID-MFM), a technique that employs an ultrathin barrier between the probe and the sample. Using fluorescently conjugated superparamagnetic nanoparticles, we demonstrate how ID-MFM can be achieved using commercially available silicon nitride windows, MFM probes and AFM equipment. The MFM signals obtained using ID-MFM were comparable to those obtained using conventional MFM. Further, samples prepared for ID-MFM were compatible with multi-modal imaging via fluorescence and transmission electron microscopy. Thus ID-MFM can serve as a high-throughput, multi-modal microscopy technique which can be especially attractive for detecting magnetism in nanoparticles and biological samples.