Charcoal-based fertilizer could be used extensively and is environmentally friendly. An experiment was designed to investigate the effects of different charcoal-based fertilizer application methods on soil microbiology and grape quality in a vineyard to guide the cultivation of ‘Shine-Muscat’. A control treatment without fertilization and six other treatments were set up. Four treatments applied carbon-based fertilizer as a base fertilizer with or without potassium fulvic acid, a complex microbial agent, or Bacillus subtilis, and two treatments were only applied with two applications of carbon-based fertilizer or compound fertilizer during the expansion period. The results showed that the bacterial phyla were mainly Proteobacteria and Bacteroidetes. Ascomycota, Basidiomycota, and Mortierellomycota dominated the fungal community. At the genus level, the composition of fungi, compared to bacteria, varied significantly, while the dominant flora differed among fertilization practices. Application of charcoal-based fertilizer enriched beneficial microorganisms, while chemical fertilizers enriched pathogenic microorganisms. The addition of microbial fungicides and biostimulants for a period reduced the size of the microbial network, lowered positive correlations, and enhanced resistance to adverse conditions and diseases and there was no significant correlation between agronomic traits and microbial network topology. A combination of soil microbial and grape agronomic traits suggests that a charcoal-based fertilizer base, with microbial fungicides applied, is the optimal fertilization regimen for grape.