Both lanthanide-containing and fluorine-containing nanomaterials present challenging targets for microbial biosynthesis because these elements are toxic to most bacteria. Here, we overcome these challenges by using an Antarctic Shewanella baltica strain that tolerates these elements and report the first biosynthesis of lanthanide-doped fluoride nanoparticles (NPs) from them. NaYF4 NPs doped with Er3+/Yb3+ are prototypical lanthanide-based upconverting nanoparticles (UCNPs) with upconverted luminescence at visible wavelengths under infrared excitation. However, their synthesis employs high precursor concentrations, organic solvents, and elevated temperatures. Microbial biosynthesis offers a greener alternative but has not been explored for these materials. Here, we harness an extremophile S. baltica strain to biosynthesize UCNPs at room temperature, based upon its high tolerance for fluoride and lanthanide ions and the observation that tolerance of lanthanides increased in the presence of fluoride. Our biosynthesis produces electron-dense nanostructures composed of Na, Y, F, Yb, and Er in the bacterial periplasm, adhered to the outer cell membrane, and dispersed extracellularly, which exhibited up-converted emission under 980 nm excitation. This suggests that extracellular or periplasmic mineralization of lanthanides as fluorides protects the bacteria from lanthanide toxicity. Subsequent heating both enhanced upconverted emission from UCNPs and allowed observation of their crystallinity in transmission electron microscopy (TEM). This work establishes the first biosynthesis of NaYF4:Yb: Er UCNPs, advancing both nanotechnology and biotechnology.