Soil quality is directly affected by alterations in its microbiological, biological, biochemical, physical, and chemical aspects. The microbiological activities of soil can affect soil fertility and plant growth because it can speed up the cycling of nutrients, enzymes, and hormones that are needed by plants for proper growth and development. The use of different agricultural management practices can influence microbial biomass and enzyme activities by altering soil microclimate, soil microorganism habitat, and nutrient cycling. Based on this, the present work planned to evaluate the impact of conventional, low-input, and organic farming systems in a vegetable field growing celery on microbial biomass and different soil enzyme activities. The present study showed a comparison of the effect of different practices on biological soil quality indicators during two sampling times, i.e., one month after colonization and one month before harvesting. It was observed that the soil microbial biomass in the organic farming system was significantly higher than that found in conventional and low-input practices. Under an organic farming system, the soil microbial biomass in December was significantly higher than that in October. The soil microbial biomass carbon in the 0–20 cm soil layer showed higher variation compared to that in the 20–40 cm layer for all the three of the farming management practices that were used in the study. Additionally, the soil total carbon and total organic carbon were recorded as being higher in the December samples than they were in the October samples. Under all the three of the management practices that were applied, the soil catalase activity was higher in the October samples than it was in the December soil samples that were collected the from 20–40 cm soil layer compared to those that were taken from the 0–20 cm layer. The application of organic fertilizer (chicken and cowmanure compost) resulted inincreases in the soil urease and in the protease activity. The protease activity of the soil samples that were extracted from the 0–20 cm and 20–40 cm soil layers in October was higher in the samples that were taken from farms using conventional practices than it was in the samples that were taken from farms using organic and low-input practices, while the samples that were collected during December from both of the soil layers showed higher protease activity when organic methods had been used. No significant variation in the soil urease activity was observed between the two soil layer samples. Urease activity was the highest when organic management practices were being used, followed by the low-input and the conventional modes. For the conventional and low-input practices, the soil urease activity showed an obvious trend of change that was related to thetime of sampling, i.e., activity in December was significantly higher than activity in October. The novelty of this study was to determine the microbial biomass carbon and enzymatic activity in a six-field crop rotation (tomato, cucumber, celery, fennel, cauliflower, and eggplant) using three management practices: low-input, conventional, and organic systems. The present study showed that the long-term application of organic fertilizers plays a large role in maintaining excellent microbial and enzyme activitythat result in improved soil quality.