Agricultural practices such as wastewater irrigation and manure application may contaminate soils with antibiotics and, consequently, lead to human health risk. The co-application of three waste-derived materials, sewage sludge (SL), Chinese medicinal herbal residues (CMHR) and biochar (BC), as a soil amendment was proposed recently for minimizing the antibiotic amount in crop tissues. The fate of six antibiotics—amoxicillin, tetracycline, sulfamethazine, norfloxacin, erythromycin and chloramphenicol—were investigated in a greenhouse soil-plant system with a fruit crop species: tomato. The pots were mixed with 5%, 10% or 20% SL-BC and SL-CMHR-BC and irrigated with wastewater with 3 μg/L or 30 μg/L antibiotics. The pot containing 20% SL-CMHR-BC captured the lowest antibiotic concentration in soils and tomato tissues. Norfloxacin was the most abundant antibiotic in the fruits, followed by tetracycline. The pot containing 20% SL-CMHR-BC significantly lowered the bioconcentration factor of the fruit, while its effects on the translocation factor were more varied. Current and some previous data were used to assess the human health risk of consuming carrot, lettuce and tomato. The estimated daily intake suggested a negligible risk to human health in general compared with the acceptable daily intake, except for CAP. A concentration of 20% SL-CMHR-BC helps minimize the human exposure risk to antibiotics contamination in edible crops.