The global environmental issue of arsenic (As) contamination in drinking water is a significant problem that requires attention. Therefore, the aim of this research was to address the application of a sustainable methodology for arsenic removal through mycoremediation aerated with micro-nanobubbles (MNBs), leading to bioscorodite (FeAsO4·2H2O) generation. To achieve this, the fungus Trichoderma atroviride was cultivated in a medium amended with 1 g/L of As(III) and 8.5 g/L of Fe(II) salts at 28 °C for 5 days in a tubular reactor equipped with an air MNBs diffuser (TR-MNBs). A control was performed using shaking flasks (SF) at 120 rpm. A reaction was conducted at 92 °C for 32 h for bioscorodite synthesis, followed by further characterization of crystals through Fourier–Transform Infrared Spectroscopy (FTIR), Scanning Electron Microscopy (SEM), and X-ray diffraction (XRD) analyses. At the end of the fungal growth in the TR-MNBs, the pH decreased to 2.7–3.0, and the oxidation-reduction potential (ORP) reached a value of 306 mV at 5 days. Arsenic decreased by 70%, attributed to possible adsorption through rapid complexation of oxidized As(V) with the exchangeable ferrihydrite ((Fe(III))4-5(OH,O)12), sites, and the fungal biomass. This mineral might be produced under oxidizing and acidic conditions, with a high iron concentration (As:Fe molar ratio = 0.14). The crystals produced in the reaction using the TR-MNBs culture broth and characterized by SEM, XRD, and FTIR revealed the morphology, pattern, and As-O-Fe vibration bands typical of bioscorodite and römerite (Fe(II)(Fe(III))2(SO4)4·14H2O). Arsenic reduction in SF was 30%, with slight characteristics of bioscorodite. Consequently, further research should include integrating the TR-MNBs system into a pilot plant for arsenic removal from contaminated water.