The present work demonstrates a novel strategy of synthesizing iron-biochar (Fe@BCSB) composite made with the waste iron bottle cap and sugar cane bagasse for implementation in the three-dimensional electro-Fenton (3DEF) process. The catalytic ability of the Fe@BCSB composite was explored to remediate the sodium dodecyl sulphate (SDS) surfactant from wastewater at neutral pH. At the optimum operating condition of Fe@BCSB dose of 1.0 g L−1, current density of 4.66 mA cm−2, and Na2SO4 dose of 50 mM, nearly 92.7 ± 3.1% of 20 mg L−1 of SDS abatement was attained during 120 min of electrolysis time. Moreover, the Fe@BCSB showed significant recyclability up to six cycles. Besides, other organics were successfully treated with more than 85% abatement efficiency in the proposed Fe@BCSB-supported 3DEF process. The total operating cost obtained during SDS treatment was around 0.31 US$ m−3 of wastewater. The phytotoxicity test revealed the positive impact of the 3DEF−treated effluent on the germination of the Vigna radiata. The electron paramagnetic resonance conveyed •OH as the prevailing reactive species for the oxidation of SDS in the 3DEF process. Further, about 81.3 ± 3.8% of SDS and 53.7 ± 4.1% of mineralization efficacy were acquired from the real institutional sewage.