The generation of energy through anaerobic digestion using animal manures is being promoted as an environmentally sustainable method of managing animal wastes. However, sustainability of biogas production is reliant on the sustainable utilization of the digestates that emanate from the process. Our study evaluated the effects of the biogas digestates on crop phytotoxicity and their fertilizer potential as a nutrient solution in hydroponic tomato production. Biogas digestates diluted up to 40% (v/v) resulted in significantly (P < 0.05) the lowest relative seed germination (RSG) in all vegetables evaluated in our study. The highest RSG was observed in the 10% biogas digestates, which was higher than the control treatment. For the crop growth study, relative to the control,the treatments with 20%, 40% and 60% mineral fertilizer substitution resulted in 39.4%; 22.8% and 8.7% significantly (P < 0.05) lower chlorophyll content, respectively. On average, the treatments with biogas slurry, though substituted with mineral fertilizers, resulted in a 275% lower fresh fruit yield compared to the control treatment. However, with biogas digestates, the sugar content in the tomato fruits significantly increased, whilst the heavy metal content was below that recommended limit when irrigation water is used. The results of our study demonstrated that cow based digestates are not a suitable nutrient media for hydroponic tomato production. Moreover, even with mineral fertilizer supplementation, only the control treatment containing only mineral hydroponic fertilizer resulted in positive growth and yield in tomatoes.