Non-standard materials used for plant fertilization, require characterization to reduce any possible undesired effects. The aim of this study was to investigate the effect of fertilization with biogas digestate (BD) and mining waste (carboniferous mudstones (MS) from coal mine) on wheat yield quality and the bioaccumulation of heavy metals in wheat grains in relation to conventional fertilization (NPK) and no fertilization. Using the co-application of waste (MS+BD), the highest yield was obtained in the first and second year, but in the third year, a slight decrease in yield was observed compared to NPK. In all years, BD and MS+BD fertilization increased the content of protein, wet gluten, and phenols in wheat grain compared to NPK and no fertilization. Waste fertilization had a positive effect on the antioxidant capacity index of grain but only in the first year. The bioaccumulation index (BAI) demonstrated that NPK decreased BAI for Zn, B, Cd, and Mn, whereas MS+BD decreased BAI for Cu, Sr, Pb, Co, Ba, and Cr.