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In this study, quartz substrates were incubated in sulfate-reducing bacteria (SRB) culture for 21 days at room temperature. Fourier transform infrared spectroscopy (FTIR) and scanning electron microscopy (SEM) were used to quantify the bacterium effect, i.e., organic metabolite acids on the wetting behavior of the mineral surface. We examined the wettability of the quartz substrate before and after microorganism effects under reservoir conditions, i.e., 0 to 27 MPa pressures and 50 °C temperature. Nevertheless, there is no study reported to date for real geologic conditions, including for hydrogen–bacteria–rock wettability, which is proven to determine storage capacities, withdrawal rates, and containment security. Our findings reveal that the pH value of quartz dipped in the nutrient solution without SRB did not change meaningfully for 21 days. However, it significantly reduced from 7.58 to 5.98 with SRB. These microorganisms produce H2S, release the organic metabolite acids, and change the wettability of the mineral. The wettability of quartz surface changes from 4.2° to 14.4°, i.e., a 10.2% increase at 27 MPa and 50 °C after the bacterium effect. FTIR indicates the hydroxyl, amine, and carboxyl group (i.e., acetic acid) spectra in the microorganism solution. Inductively coupled plasma mass spectrometry (ICP-MS) shows that the concentrations of sulfate ( normalS normalO 4 2 − ), aluminum (Al), iron (Fe), calcium (Ca), and magnesium (Mg) have significantly reduced after the SRB effect. Overall, strong water-wet quartz shifted to less water-wet quartz after the microorganism effect under the reservoir conditions. SRB slightly reduce the residual trapping effect. Hence, this process might have enhanced the withdrawing efficiency of H2 in high brine-saturated sandstone reservoir rock under the microbial activity.