Anaerobic digestion has been recently proposed as a more sustainable energy supply chain able to strengthen the existing security of supply provisions. Anaerobic digestate (AD) is the by-product of the anaerobic digestion process and presents organic fertilizer characteristics, but its agronomic usage has been hindered by both agronomic and environmental concerns. In this study, the impact of agricultural liquid (LD) and solid (SD) AD and beef manure (Man) was evaluated on some agro-environmental characteristics. First, the AD fractions functional groups were characterized by FT-IR, and then LD and SD performances were evaluated on soil organic carbon (SOC) stock and carbon dioxide (CO2) emissions and compared to beef manure (Man). The fertilizer impact was also considered with the presence or absence of a shallow water table. Results showed that SD increased of ca. 3 t ha−1 the SOC stock in the 0–20 cm soil profile with respect to LD, while it was comparable to Man despite the lower C input (1.7 vs. 8.7 t C ha−1), due to the presence of more stable compounds (e.g., lignin). The CO2 fluxes were affected by both fertilizer type and water table level. In the absence of a water table, the CO2 emissions (5.5 g CO2 m2 d−1) were driven by carbon content and quality in the fertilizer, while the presence of a shallower water table hindered mineralization of stable SOC and, in turn, reduced emissions (4.4 g CO2 m2 d−1). AD can be considered a beneficial solution to both maintain soil fertility and, at the same time, give new insight into a circular economy model, although further investigation on GHG emissions is required.