Background The Atacama salt flat is located in northern Chile, at 2300 m above sea level, and has a high concentration of lithium, being one of the main extraction sites in the world. The effect of lithium on microorganism communities inhabiting environments with high concentrations of this metal has been scarcely studied. A few works have studied the microorganisms present in lithium-rich salt flats (Uyuni and Hombre Muerto in Bolivia and Argentina, respectively). Nanocrystals formation through biological mineralization has been described as an alternative for microorganisms living in metal-rich environments to cope with metal ions. However, bacterial lithium biomineralization of lithium nanostructures has not been published to date. In the present work, we studied lithium-rich soils of the Atacama salt flat and reported for the first time the biological synthesis of Li nanoparticles. Results  Bacterial communities were evaluated and a high abundance of Cellulomonas, Arcticibacter, Mucilaginibacter, and Pseudomonas were determined. Three lithium resistant strains corresponding to Pseudomonas rodhesiae, Planomicrobium koreense, and Pseudomonas sp. were isolated (MIC > 700 mM). High levels of S2− were detected in the headspace of P. rodhesiae and Pseudomonas sp. cultures exposed to cysteine. Accordingly, biomineralization of lithium sulfide-containing nanomaterials was determined in P. rodhesiae exposed to lithium salts and cysteine. Transmission electron microscopy (TEM) analysis of ultrathin sections of P. rodhesiae cells biomineralizing lithium revealed the presence of nanometric materials. Lithium sulfide-containing nanomaterials were purified, and their size and shape determined by dynamic light scattering and TEM. Spherical nanoparticles with an average size < 40 nm and a hydrodynamic size ~ 44.62 nm were determined. Conclusions We characterized the bacterial communities inhabiting Li-rich extreme environments and reported for the first time the biomineralization of Li-containing nanomaterials by Li-resistant bacteria. The biosynthesis method described in this report could be used to recover lithium from waste batteries and thus provide a solution to the accumulation of batteries.