Digestate from biogas production can be recycled to the soil as conditioner/fertilizer improving the environmental sustainability of the energy supply chain. In a three-year maize-triticale rotation, we investigated the short-term effects of digestate on soil physical, chemical, and microbiological properties and evaluated its effectiveness in complementing the mineral fertilizers. Digestate soil treatments consisted of combined applications of the whole digestate and its mechanically separated solid fraction. Digestate increased soil total organic C, total N and K contents. Soil bulk density was not affected by treatments, while aggregate stability showed a transient improvement due to digestate treatments. A decrement of the transmission pores proportion and an increment of fissures was observed in digestate treated soils. Soil microbial community was only transiently affected by digestate treatments and no soil contamination from Clostridiaceae-related bacteria were observed. Digestate can significantly impair seed germination when applied at low dilution ratios. Crop yield under digestate treatment was similar to ordinary mineral-based fertilization. Overall, our experiment proved that the agronomic recycling of digestate from biogas production maintained a fair crop yield and soil quality. Digestate was confirmed as a valid resource for sustainable management of soil fertility under energy-crop farming, by combining a good attitude as a fertilizer with the ability to compensate for soil organic C loss.