A large amount of glyphosate enters the soil at a high frequency, forming “pseudo-persistent” pollutants that, in turn, threaten soil ecological function and crop growth. Earthworm casts (EWCs) are a sound organic alternative to chemical fertilizers to promote crop growth. Dissolved organic matter from EWCs (EWC-DOM) is supposed to be a more mobile and bioavailable fraction. However, the effect of EWC-DOM on the phytotoxicity of glyphosate remains largely unknown. This study examines glyphosate-induced oxidative stress and its impact on antioxidant and detoxification enzymes in citrus plants grown in soils with and/or without EWC-DOM. The results suggest that EWC-DOM could reduce the membrane lipid peroxidation level, thus slowing down the aging of plants in order to maintain stronger resilience, with more active antioxidant enzymes (including SOD, POD, and CAT) and detoxification enzymes (including GST, laccase, CPR, and UGTs) that could effectively remove reactive oxygen species (ROS) caused by glyphosate stress, thereby alleviating the damage of ROS accumulation on plant tissues. Our data indicate that incorporating EWC-DOM should be a sound way to protect citrus plants from the phytotoxicity caused by using glyphosate for orchard weeding. This has major implications for the sustainable and healthy development of citrus production.