When an earthquake occurs, magnetic minerals are formed in the gouge under the combined action of frictional heating and fluid. Generally, the gouge is altered, and a detailed analysis of neoformed minerals is difficult. The Taiwan Chelungpu fault Drilling Project provided continuous records of the active Chelungpu fault gouges. By analyzing the magnetic parameters along the 16 cm thick gouge which houses the principal slip zone of the 1999 Chi-Chi earthquake (M w 7.6), we observed a 4 cm shift between the maximum of magnetic susceptibility and the maximum of remanence. The maximum magnetic susceptibility is localized along the principal slip zone. The main identified magnetic minerals are magnetite and goethite, which have very different magnetic parameters. We propose that the maximum of the concentration of magnetite and goethite corresponds to the maximum of magnetic susceptibility and remanence, respectively. By modeling the concentration of these two magnetic minerals, we explain satisfactorily the profiles of magnetic susceptibility and remanence. This quantitative modeling indicates that~200 ppmv of magnetite formed in the principal slip zone and its main contact area. Similarly,~1% of goethite is formed in the center of the gouge, where the fluids are more enriched in iron. We propose that the magnetite and goethite are formed and altered during seismic cycles.