The application of organic manure is an effective way to develop sustainable agriculture. However, the application of organic manure may be associated with a potential risk of heavy metal pollution for soil and crops. In this study, the effects of organic cow manure (T1) (as base fertilizer), organic pig manure (T2) (as base fertilizer) and chemical fertilizer (T3) on winter wheat grain yields, grain quality, heavy metal concentrations and heavy metal bioconcentration factors (BCFs) in a soil–wheat system were studied from November 2021 to June 2023. The results showed that the winter wheat grain yields in the T1 and T2 treatments were lower than those in the T3 treatment by 2.57–38.0% and 10.5–25%, respectively. There were no significant differences in quality indexes of winter wheat grain among different fertilizer treatments. The concentrations of heavy metals in topsoil and winter wheat were 0.12–76.11 μg/g and 0.01–43.25 μg/g, respectively. The BCFs of heavy mental in the soil–wheat grain system was 0–2.92. In general, there were no significant differences in heavy metals’ concentrations in topsoil and wheat grain among different fertilizer treatments. In summary, compared with chemical fertilizer, the short-term application of organic manures had no significant effect on heavy metals concentrations in topsoil and wheat.