Bacteria quickly acquire the ability to survive or grow in the presence of an antibacterial agent that should be able to inhibit or kill them, leading to increased mortality caused by infective diseases. The digestate from the anaerobic digestion (AD) of the organic fraction of municipal solid waste (OFMSW) is spread on soil, but the knowledge on the presence and persistence of the antibiotic resistance genes (ARGs) is limited. Thus, this study aims to evaluate the presence of seven ARGs (bla_TEM, bla_OXA, ermB, qnrB, sulI, sulII, tetA, and tetW) in the OFMSW and their persistence after the AD, using the innovative droplet digital Polymerase Chain Reaction (ddPCR), not yet used on this matrix. A total of 31 samples were collected from the influent and effluent of the AD in two plants located in Northern Italy. ARG concentration ranged between 4 and 9 Log gene copies/kg of sludge. A limited reduction in the concentration of antibiotic resistance targets given by AD was observed in the study (<1 Log). The persistence of ARGs after mesophilic digestion of the OFMSW suggests a risk of horizontal transmission when directly spread on soil. Further evaluations are needed for safe and sustainable reuse of such sludges.