Microbial communities have been shown over the last few years to be a significant component of the subseafloor crustal environment. However, their role in the low-temperature alteration of seafloor basalts remains an open question. Among the diversity of microorganisms that can contribute to oceanic rock weathering, sulfate-reducing bacteria have been suggested, based on sulfur isotope studies, to be major actors. Previous laboratory experiments conducted on basalt samples from the Juan de Fuca Ridge incubated with model sulfate-reducing bacteria for several months showed that bacterial activity can play a role in the decrease of seafloor magnetic signal. In this paper, we characterized alteration features at the nanoscale in one of these basalt samples in order to better understand the mechanisms of the magnetic signal decrease. For that purpose, we used a combination of focused ion beam milling, transmission electron microscopy and scanning transmission X-ray microscopy. Fossilized microbial cells and phyllosilicates were evidenced at the surface of the sample. Within the sample, alteration rims mostly composed of Fe and S and measuring 100–300 nm in thickness were observed around titanomagnetites crystals that bear most of the magnetic signal. In contrast, these features were not observed on noninoculated control samples. This study offers a detailed view of the specific mineral assemblages formed in the presence of model sulfate-reducing bacteria that can be looked for in the oceanic crust. These observations contribute to understand the potential role of microbes in the alteration of the oceanic crust.