Using waste for plant fertilization requires identifying and reducing any possible undesired effects. The aim of this study was to investigate the effect of fertilization with biogas residue (BD) and mining waste (carboniferous mudstone and clay rock from a coal mine – MS) on oilseed rape (OSR) health quality of seeds in relation to conventional fertilization (NPK) and no fertilization. In the first and second years of the study the highest seed and fat yield was obtained from the NPK treatment. However, in the third year the highest yield was found using MS+BD. The lowest glucosinolate content was determined in OSR seeds fertilized with MS in the second year. The ratio of omega-6/omega-3 FA varied in a narrow range from 2.15 (NPK and MS) to 2.21 (BD and MS+BD). The most preferred form of fertilization in reducing heavy metal bioaccumulation (BAI) in seeds was MS+BD and NPK. NPK fertilization primarily reduced BAI of Zn, B, Mn, Cd, Co, and Fe, whereas MS+BD reduced BAI of Cu, Sr, Cr, Ba, and Pb. Results suggest that the wastes evaluated can be an interesting alternative for conventional fertilization in tested soil without the risk of a significant decrease in OSR quality.