The occurrence of seven trace elements and forty three antibiotics was investigated in manure-based fertilizers from the Zhejiang province of China. These trace elements included copper, zinc, arsenic, chromium, mercury, lead and cadmium. The targeted antibiotics included four groups: sulfonamides, tetracyclines, fluoroquinolones and chloramphenicols. The median amounts of copper, zinc, arsenic, chromium, mercury, lead and cadmium in the analyzed samples were 160, 465, 7.9, 21.2, 0.3, 8.1 and 0.6mg·kg−1, respectively. Seventeen antibiotics were detected. Enrofloxacin was the most frequently detected compound, with a detection rate of 39.3% and concentrations ranging from 6.7μg·kg−1 to 4091μg·kg−1. Based on the referred loading rates in agricultural soil, 10% of the collected manure-based fertilizer samples might pose a high potential ecological risk due to the presence of antibiotics. Occurrence of seven trace elements and forty three antibiotics was investigated in manure-based fertilizers in Zhejiang province of China. The trace elements included copper, zinc, arsenic, chromium, mercury, lead and cadmium; the targeted antibiotics included four groups: sulfonamides, tetracyclines, fluoroquinolones and chloramphenicols. The medium values of copper, zinc, arsenic, chromium, mercury, lead and cadmium in the analyzed samples were 160, 465, 7.9, 21.2, 0.3, 8.1 and 0.6mg·kg−1, respectively. Seventeen antibiotics were detected. Enrofloxacin was the most frequently detected compound with the detection rate of 39.3% and the concentrations ranged from 6.7μg·kg−1 to 4091μg·kg−1. Based on the referred loading rates, 10% of the collected manure-based fertilizers might pose a high potential ecological risk after their application onto agriculture soil due to the presence of antibiotics. Display omitted •Antibiotics and trace elements were investigated in manure-based fertilizers.•64% of manure-based fertilizers were positively detected with at least one drug.•Enrofloxacin was the most frequently detected compound with detection ratio at 39%.•10% fertilizers might pose a high potential ecological risk after application on soil.