Serious contamination of perfluorooctanoic acid (PFOA) has aroused global concern. General biotransformation or iron-based materials did not meet efficient PFOA elimination. Here, specific green and low-carbon microorganism-biochar pellets, multi-component and multifunctional iron-sulfur (FexSy) mineral pellets, and a microbe-FexSy interaction device were developed to solve this problem. The multi-scale (molecular, interface, and column scales) research method combined with the multi-process reaction model was constructed to explore PFOA removal mechanism. Results revealed that microbe-FexSy interaction achieved excellent PFOA degradation performance and retention effect, with degradation rate λ (0.213 h−1) increased by 113 % than FexSy (0.100 h−1) device. The distribution coefficient Kd and kinetic adsorption α increased by 18.54 % and 22.61 %; the fraction of kinetic sorption increased by 63.83 % in microbe-FexSy device (77 %) than alone FexSy (47 %) device. Delftia and Pseudomonas combined with Fe2+ drove an efficient cycle chain reaction for PFOA. Quantitative structure–activity relationship (QSAR) model prediction results indicated that intermediates exhibited lower biotoxicity than PFOA. Furthermore, NO3– further increased the retention effect of microbe-FexSy device for PFOA with little reaction rate fluctuation, making it promising for eliminating PFOA contamination, especially in NO3– type of groundwater. It provided an efficient technology and device based on microbe-mineral interaction in remediating PFOA-contaminated groundwater.