Continuous low-cost bulk biolixiviant production remains as one of the main challenges of heterotrophic bioleaching towards large scale application. This study aimed at developing non-aseptic Gluconobacter oxydans-amended fluidized-bed reactor (FBR) process for continuous production of gluconic acid for efficient leaching of rare earth elements (REEs) and base metals from spent nickel-metal-hydride (NiMH) batteries. In preliminary experiments, the FBR became contaminated and massively overgrown by air-borne fungus, Leptobacillium leptobactrum. In a series of batch bioassays, operational conditions were investigated to discourage the fungal activity i.e., an ecologically engineered niche for gluconic acid production. High gluconate concentration (≥100 g/l) and/or low pH (≤2.5) gave a selective preference for G. oxydans growth over L. leptobactrum and controlled the activity of possible contaminants during FBR continuous operation. The highest gluconic acid production rate of 390 g/l∙d with corresponding glucose-to-gluconic acid conversion yield of 94% was obtained at hydraulic retention time (HRT) of 6.3 h and 380 g/l∙d glucose loading rate. Using the FBR effluents as leaching agents, respectively, total base metals and REEs leaching yields of up to 82% and 55% were achieved within 7 days at 1% (w/v) spent battery pulp density. The obtained glucose-to-gluconic acid conversion rates and yields were one of the highest reported for any glucose biotransformation process. The REE leaching yields were higher than those reported for similar high metal-grade REE secondary sources. The high-rate glucose-to-gluconic acid bioconversion in the non-aseptic system utilizing microbial ecology based FBR operation strategy rather than aseptic chemostats indicates industrial feasibility of gluconic acid production and thus, the applicability of heterotrophic bioleaching.