Abstract. Magnetite is a widespread ore mineral in skarn systems and usually hosts a wide variety of inclusions. Micro- to nano-sized solid inclusions in magnetite are unique tools to track the evolutionary processes of its host mineral and, subsequently, to constrain the timing of the mineralization event. In this study, we characterize micro- to nano-sized solid inclusions in magnetite from the La Víbora magnesian skarn (Málaga, Spain) using scanning electron microscopy (SEM) and transmission electron microscopy (TEM). TEM energy-dispersive X-ray spectrometry (EDS) analyses and compositional mapping expose two types of nano-inclusions oriented along the (111) of magnetite: type 1 includes dolomite, spinel, and Mg–Fe–Al silicate, and type 2 is made up of Mg–Fe–Al silicates enveloping the Mg-bearing amorphous silica phase. High-resolution transmission electron microscopy (HRTEM), selected-area electron diffraction (SAED), and fast Fourier transform (FFT) patterns reveal that the majority of the solid inclusions display non-oriented matrices compared to the host magnetite, precluding the possibility of sub-solidus processes. Instead, these inclusions are thought to preserve skarn mineral assemblages that were entrapped during the growth of magnetite. However, the local supersaturation of fluids trapped in the boundary layer of crystallizing magnetite is evidenced by coherent lattice orientation of precipitated and host magnetite and by the occurrence of an Mg-bearing amorphous silica phase. Our findings reveal that skarn reactions observed at field and microscopic scales are also recorded in nano-sized inclusions within magnetite. These observations underscore the significance of micro- to nano-scale solid inclusions in magnetite to decipher overprinted skarn reactions as well as constraining the timing of Fe mineralization events in skarns.