Alkaline organic residues, such as wood ash (WA), deinking paper sludge (DPS), and mixed paper sludge (MPS) could have a significant potential for mitigating greenhouse gases (GHG) when they are used for land application. The DPS was mixed and then granulated with MPS, WA and/or composted DPS to form pellets. A 56-d incubation study was carried out to investigate the effect of alkaline organic residue pellets on: (1) the biological and chemical properties of acidic clayey soil; (2) on carbon dioxide (CO2), on methane (CH4), and nitrous oxide (N2O) soil emissions. The experimental design included eight different treatments: unfertilized control (Control), fertilized control with mineral nitrogen (controlF), and six pelleted alkaline organic residue amendments (T1–T6) combined with mineral nitrogen fertilizer. The six amendments were: (T1) 100% DPS; (T2) 100% composted [50% poultry manure and 50% T1]; (T3) 50%WA + 50% T1; (T4) 50% WA + 50% T2; (T5) 50%T2 + 30%WA + 20% MPS; (T6) 50% T1 + 30%WA + 20% MPS. The results showed that alkaline residues significantly increased soil pH, the concentration of water-extractable organic carbon, and water-extractable nitrogen. Alkaline treatments had a positive effect on soil microbial activity. The highest mitigation efficiency of cumulative CO2 was obtained with T4, which released 10% less CO2 than other treatments. No significant effect on cumulative CH4 emissions was observed. Total cumulative N2O emissions were reduced by 37% with T5. Our study also showed that organic pellets based on alkaline residues improved the soil properties and can play a role in the mitigation of GHG in acidic clayey soil. Therefore, the co-application of alkaline organic residue pellets with chemical fertilizer might be considered as a sustainable approach in agriculture.