The emerging need for sustainable management of the increasing quantities of urban and industrial organic wastes creates opportunities for the development of alternative strategies for the improvement of degraded soils. The current study was performed to examine the effects of agricultural wastes application on soil bacterial community as well as CO and NO direct gas emissions. Untreated soils were compared with soils, which received the same amount of N (100 μg/g soil) in the form of ammonium nitrate and organic agricultural waste. In particular, soils were incubated with three different organic agricultural wastes, orange (OP), mandarin (MP) and banana peels (BP) and ammonium nitrate (F) after adjusting soil water at 70% of its holding capacity. In the current study, soil chemical characteristics, quantitative PCR of denitrifiers (nirK, nirS, nosZI and nosZII) and16s rRNA amplicon sequencing were assessed to examine the links between the soil microbial communities and short-term soil direct NO emissions when treated with agricultural wastes. The highest soil direct NO emissions were recorded in soils received ammonium nitrate while soils received agricultural wastes exhibited substantially lower soil direct NO emissions. On the contrary, agricultural wastes stimulated CO accumulation as well as the growth of copiotrophic bacterial groups like Proteobacteria and Firmicutes. Interestingly, direct soil NO emissions were decoupled from the density of denitrifier community while agricultural wastes caused a substantial reduction of the relative abundance of bacterial taxa associated with NO emissions in the soil. This study proves evidence that agricultural wastes could be integrated in a waste management strategy, which inter alia includes their direct use in agricultural ecosystems resulting in reduced NO emissions.