Integrated crop-livestock (ICL) and integrated crop–livestock–forest (ICLF) systems have the potential to improve soil quality, and the use of organic fertilizers may further enhance soil carbon (C) and nitrogen (N) accumulation, microbial activity, and crop productivity. Our objective was to evaluate soil C and N inputs and their effect on C and N dynamics, microbial attributes, and maize production in ICL and ICLF systems with the application of inorganic and organic fertilizers of animal origin. Established in 2015, the experiment consisted of a randomized block design with a 2 × 4 factorial arrangement, including ICL and ICLF systems and four fertilization strategies: (i) without fertilization, (ii) inorganic, (iii) poultry litter, and (iv) swine manure, with three replicates, evaluated during the 2018 and 2019 growing seasons. Soil C and N contents, microbial communities, planta C and N inputs, and maize yield were evaluated. The strongest responses to fertilization occurred in the 0–10 cm layer, where soil C and N stocks increased from 21.0 to 46.2 Mg ha⁻¹ and from 1.4 to 4.9 Mg ha⁻¹, respectively. Although some treatment-specific differences were observed, overall differences between the two production systems were limited during the study period. Within both integrated systems, organic and inorganic fertilization increased Gram-positive and Gram-negative bacteria, actinomycetes, saprophytic fungi and the fungi:bacteria ratio. Poultry litter and swine manure increased maize yield by approximately 25% in 2017/2018, whereas poultry litter fertilization increased yield by about 12% in 2018/2019. Strong positive correlations among soil C, N, and microbial groups indicate a close linkage between nutrient accumulation and microbial community development; however, these attributes were not directly associated with maize yield. Short-term forest inclusion resulted in limited differences between ICL and ICLF, whereas fertilization increased soil C and N accumulation and microbial attributes in both systems.