Integrated crop-livestock systems (ICLS) in paddies are an important strategy to reduce fertilizer requirements of rice (Oryza sativa). Legume crop rotations and fertilization increase soil carbon (C) and nitrogen (N) availability compared to rice monocropping. Our objectives were to evaluate the effects of fertilization, namely P and K, in no-till ICLS of continuously flooded rice and rice-soybean rotation in subtropical paddy fields on: (i) soil microbial community, (ii) labile C and N pools, (iii) microbial groups, and (iv) rice yield. Both ICLS were annual ryegrass pastures under beef cattle grazing during the winter season without tillage. Although flooded rice yield did not respond to P and K fertilization in either ICLS, P and K fertilization increased microbial biomass C and N content, and permanganate-oxidizable C (POxC) by 37%, 36%, and 42%, respectively, in both production systems, due to alleviation of nutrient limitation for microbial growth. ICLS under soybean-rice rotation had higher C availability and 22.4% higher rice yield than the rice monocropping. Positive relationships were observed between microbial biomass N and Gram-positive (G+; R-2 = 0.61), Gram-negative (G-; R-2 = 0.54) bacteria, and saprophytic fungi (R-2 = 0.45). However, total fungi was almost 10 times lower than the PLFA of total bacteria on average of cropping systems. G+ bacteria were the only microbial group correlated with N availability under flooded rice. We conclude that P and K fertilization has a direct impact on the microbial community and biomass and consequently on the C and N availability, but does not increase rice yield under no-till ICLS. Soybean-rice rotation yields more than rice monocropping system under ICLS and soil bacteria are more sensitive than saprophytic fungi to changes in soil nutrient status during flooding period in paddy fields.