Integrated crop-livestock-forestry systems are promising alternatives to landscape impoverishment caused by monoculture systems. However, nutrient management in integrated systems still needs to be more comprehensively resolved. As soil microbial biomass (MB) is a soil nutrient reservoir that can contribute to crop nutrition, this study aimed to understand the relationship between C and N of soil MB (CMB and NMB, respectively), N nutrition index (NNI), and crop yield in monoculture and integrated crop-forestry, crop-livestock, and crop-livestock-forestry systems to propose management strategies for N-fertilization in these systems. The systems were established in an experiment conducted in 2012 at the Center for Technological Innovation in Agriculture (Portuguese acronym: NITA) under a randomized block design with three repetitions using crop (maize), livestock (Angus beef cattle), and forestry (eucalyptus) components. Measurements were performed in 2019. The systems showed satisfactory CMB and NMB values; however, the crop-forestry system presented higher CMB (338.7 mg kg⁻¹) compared with that of the monoculture system (272.7 mg kg⁻¹). NMB was increased by 22% after N-fertilization in all systems, and it was higher in the crop-livestock and crop-livestock-forestry systems probably as a result of the deposition of N-rich livestock urine. N-fertilization also increased crop yield and NNI in the monoculture system, but not in the crop-forestry system, probably because trees formed a shady ecosystem that limited plant growth. Thus, the results indicate that N-fertilization tables should consider the specific edaphoclimatic conditions of integrated crop-livestock-forestry systems to avoid excessive N-fertilization rates.