Glyphosate-based herbicides (GBH) are the most widely used pesticides globally. Their persistence in soils and effects on non-target organisms have become a concern in agricultural and natural ecosystems. We experimentally studied, whether residues of GBH (Roundup Gold) or pure glyphosate in soils affect the germination or sprouting and growth of crop plants after the safety period. The seed germination of faba bean, oat and turnip rape, and sprouting of potato tubers was delayed in the greenhouse experiments in soils treated with GBH or with pure glyphosate. The total shoot biomass of faba bean was 28%, oat 29% and turnip rape 58% higher in control compared to GBH soils four weeks after sowing. In the beginning of the growing season, the plant growth in the field experiment supported the observations in the greenhouse experiment. However, at the end of the field experiment, potato shoot biomass was 25% and tuber biomass 14% greater in GBH soil compared to control soil. Potato tubers tended to gather low amounts of glyphosate (0.02 mg/kg) and its metabolite AMPA (0.07 mg/kg). Grazing by barnacle geese was three times higher in oats growing in the GBH soils compared to control oats in the field. Our results draw attention to complex indirect effects of GBH on crop plant seedling establishment and resistance to herbivores.