Labile soil organic matter pools (LSOMp) are believed to be the most sensitive indicator of soil quality when it is changed rapidly with varied management practices. In sub-tropical climates, the turnover period of labile pools is quicker than in temperate climates. Organic amendments are of importance in improve the LSOMp for a temperate climate and may be helpful in sub-tropical climates as well. Hence, the status of LSOMp was studied in long term farmyard manure (FYM) amended soils under wheat (Triticum aestivum L.) and pearl millet (Pennisetum glaucum L.) cropping systems in sub-tropical arid conditions. At the same time, we also attempt to determine the impact of mineral nitrogen (N) application in these pools. In this study, dissolved organic matter (DOM), microbial biomass (MB), and light fraction (LF) were isolated in the management practices involving different modes and rates of FYM applications along with the application of nitrogenous fertilizer. C and N contents of the labile pools were analyzed in the soil samples at different periods after FYM applications. Among the different pools, microbial biomass carbon (MBC) and dissolved organic carbon (DOC) were changed significantly with different rates and modes of FYM application and mineral N application. Application of FYM at 15 Mg ha−1 in both the seasons + 120 kg ha−1 mineral N resulted in significantly higher MBC and DOC as compared to all of the other treatments. This treatment also resulted in 13.75% and 5.8% more MBC and DOC, respectively, as compared to the amount of MBC and DOC content in the control plot where FYM and mineral N were not applied. Comparing the labile organic matter pools of 45 years of FYM amendment with initial values, it was found that the dissolved organic carbon, microbial biomass carbon, and light fraction carbon were increased up to the maximum extent of about 600, 1200, and 700 times, respectively. The maximum amount of DOM (562 mg kg−1 of DOC and 70.1 mg kg−1 of DON), MB (999 mg kg−1 of MBC and 158.4 mg kg−1 of MBN), LF (2.61 g kg−1 of LFC and 154.6 g kg−1 of LFN) were found in case of both season applied FYM as compared to either summer or winter applied FYM. Concerning the different rates of FYM application, 15 Mg ha−1 FYM also resulted in a significantly higher amount of DOM, MB, and LF as compared to other FYM rates (i.e., 5 Mg ha−1 and 10 Mg ha−1). Amongst different pools, MB was found to be the most sensitive to management practices in this study. From this study, it was found that the long-term FYM amendment in sub-tropical soil along with mineral N application can improve the LSOMp of the soil. Thus, it can be recommended that the application of FYM at 15 Mg ha−1 in summer and winter with +120 kg ha−1 mineral N can improve SOC and its labile pools in subtropical arid soils. Future studies on LSOMp can be carried out by considering different cropping systems of subtropical climate.