Organic amendments favor the development of sustainable agriculture by using less chemical fertilizers. In this way, the use of digestates from anaerobic digestion as soil conditioners in agriculture has been gaining interest due to their important N and P nutrient contents, among others. This study evaluated the potential use of digestates from anaerobic reactors treating food waste in single (D1) and two-stages (D2: hydrolytic/acidogenic and D3: acetogenic/methanogenic) configurations. Digestate characteristics and their potential application conditions (100, 50, 25, and 5%) were evaluated using Raphanus sativus as an indicator species. D3 reported the best performance in terms of: (i) better physicochemical, microbiological, and parasitological characteristics, being a class B material, without exceeding the established limits for heavy metals, fecal coliforms (FC < 1000 CFU 100 mL− 1), Salmonella spp. (0 CFU g− 1), and viable helminth eggs (0 HE g− 1); (ii) better stability indicators on D3, followed by D1 (volatile solids/total solids (VS/TS): 0.57 and 0.65, pH: 8.63 and 6.80, respectively), while D2 was the most unstable digestate (VS/TS > 0.87 and acidic pH); and (iii) greater potential for agricultural use, since a 5% dose produced a germination index > 120%, whose effect is associated with the presence of humic and fulvic acids and with N and P concentrations > 1%. In addition, the study reported that volatile fatty acids > 2500 mg L− 1 act as antimicrobial agents, reducing the required pathogen removal pretreatments.