Biochar adsorption has emerged as a favorable and environmentally friendly approach for removing metals such as chromium (Cr) from wastewater. However, the use of pristine biochar (PBC) is limited due to its finite adsorptive capacity, selectivity, and potential for secondary pollution. In this study, a novel bifunctionalized magnetic biochar (BMBC) was fabricated by incorporating cystamine as a ligand and glutaraldehyde as a crosslinker into alkali-treated magnetic biochar (MBC). This chemical modification introduced numerous amino groups and disulfide bonds onto the surfaces of BMBC. The biochar adsorbents’ surface morphologies, crystal structures, and texture properties were characterized using SEM, XRD, and N2 adsorption-desorption techniques. The specific surface area was determined using the BET method. Furthermore, the surface functional groups and elemental compositions before and after adsorption were analyzed using FTIR and XPS, respectively. The results demonstrated higher Cr(VI) removal efficacy of BMBC (100%) than MBC (72.37%) and PBC (61.42%). Optimal conditions for Cr(VI) removal were observed at a solution pH of 2, a temperature of 50 °C, a reaction time of around 1440 min, and an initial adsorbate concentration of 300 mg/L. The sorption process followed a chemical mechanism and was controlled by monolayer adsorption, with a maximum adsorption capacity of 66.10 mg/g at 50 °C and a pH of 2, as indicated by the larger fitting values of the pseudo–second-order and Langmuir models. The positive ∆Ho and ∆So values and negative ∆G0 values suggested a spontaneous and endothermic Cr(VI) adsorption process with high randomness at the solid/liquid interface. The removal of Cr(VI) was attributed to the reduction of Cr(VI) into Cr(III) facilitated by the introduced amino acids, sulfur, and Fe(II), electrostatic interaction between Cr(VI) in the solution and positive charges on the adsorbent surface, and complexation with functional groups. The presence of co-existing cations such as Cu(II), Cd(II), Mn(II), and K(I) had little effect on Cr(VI) removal efficiency. At the same time, the co-existence of anions of Cl−, NO3−, SO42−, and HPO42− resulted in a 7.58% decrease in the Cr(VI) removal rate. After five consecutive adsorption/desorption cycles, BMBC maintained a high Cr(VI) removal rate of 61.12%. Overall, this novel BMBC derived from rice straw shows great promise as a biosorbent for treating Cr(VI) in wastewater.