Ammonia (NH3) volatilization from animal manure application is detrimental to the environment, crop nutrition and human health and investigations into mitigation strategies are a great challenge among agro-environmental issues. The objective of the present study was to reduce NH3 volatilization in a paddy soil fertilized with anaerobically digested cattle slurry (ADCS). In laboratory experiments, several mitigation methods for NH3 volatilization were tested. Among these methods, acidification of ADCS with wood vinegar (WV) from pH 7.8 to pH 6.0 was the most effective in suppressing NH3 volatilization. Increasing the depth of the floodwater threefold also reduced NH3 volatilization by more than 80%. A lysimeter (1 m square with 0.5 m depth) experiment was conducted in triplicate with the following treatments: (1) chemical fertilizer ([CF] N:P:K = 14:14:14), (2) ADCS, (3) acidifying ADCS with WV to pH 6.0, (4) keeping a deeper floodwater level (DFW) at 10 cm at the ADCS applications (3–4 cm in the other treatments). A total fertilization of 30 g –N m−2 (basal and three times as a top dressing) was done for all treatments either with CF or ADCS and other fertilizations were not conducted. The NH3 volatilization was measured using the dynamic flow chamber method for 1 week after each fertilizer application. The results highlighted that the use of ADCS, instead of CF, enhanced NH3 volatilization approximately eightfold, and the total amount of NH3 volatilization corresponded to 13% of the applied –N in the ADCS treatment. This increased N loss was effectively (63–82%) reduced by adding WV and by keeping the floodwater level deeper. Biomass production was not significantly different between the CF (2880 ± 226 g [dry basis] m−2) treatment and the three ADCS treatments (3320 ± 249, 2720 ± 384 and 3330 ± 359 g [dry basis] m−2 in the ADCS, ADCS + WV and ADCS + DFW treatments, respectively). These results demonstrated that enhanced NH3 volatilization in soil fertilized with ADCS was mitigated by the simultaneous application of an acid residue, such as WV, and by the management of the floodwater level.