Anaerobic digestion has been suggested as an intervention to attenuate antibiotic resistance genes (ARGs) in livestock manure but supporting data have typically been collected at laboratory scale. Few studies have quantified ARG fate during full-scale digestion of livestock manure. We sampled untreated manure and digestate from seven full-scale mesophilic dairy manure digesters to assess ARG fate through each system. Samples were collected biweekly from December through August (i.e., winter, spring, and summer; n = 235 total) and analyzed by quantitative polymerase chain reaction for intI1, erm(B), sul1, tet(A), and tet(W). Concentrations of intI1, sul1, and tet(A) decreased during anaerobic digestion, but their removal was less extensive than expected based on previous laboratory studies. Removal for intI1 during anaerobic digestion equaled 0.28 ± 0.03 log₁₀ units (mean ± SE), equivalent to only 48% removal and notable given intI1’s role in horizontal gene transfer and multiple resistance. Furthermore, tet(W) concentrations were unchanged during anaerobic digestion (p > 0.05), and erm(B) concentrations increased by 0.52 ± 0.03 log₁₀ units (3.3-fold), which is important given erythromycin's status as a critically important antibiotic for human medicine. Seasonal log₁₀ changes in intI1, sul1, and tet(A) concentrations were ≥50% of corresponding log₁₀ removals by anaerobic digestion, and variation in ARG and intI1 concentrations among digesters was quantitatively comparable to anaerobic digestion effects. These results suggest that mesophilic anaerobic digestion may be limited as an intervention for ARGs in livestock manure and emphasize the need for multiple farm-level interventions to attenuate antibiotic resistance.