Biochar application to soil is widely recognized as a promising agricultural management practice to increase crop production by enhancing the physical, chemical, and microbiological properties of the soil. Despite the fact that numerous studies have investigated biochar production and alterations in soil properties, the effects of biochar on contrasting soils within the same region remain poorly understood, especially for semi-arid regions. Therefore, a three-year field experiment was initiated in 2020 wherein biochar was applied once to a buckwheat field at rates of 0, 20, 40, and 60 Mg ha−1 (BC0: no biochar; BC1: 20 Mg ha−1; BC2: 40 Mg ha−1; BC3: 60 Mg ha−1) for two soil types (aeolian sandy and grey meadow soil) in the northeast of Inner Mongolia, China. The soil water storage (SWS), nutrient contents (organic matter, available nitrogen, phosphorus, and potassium), microbial biomass (carbon, nitrogen, and phosphorus), and enzyme activities (urease, invertase, and alkaline phosphatase) were assessed at a soil depth of 0–15 cm as part of the soil quality assessment, and the buckwheat grain yield was estimated for crop productivity evaluation. The results showed that biochar amendment improved selected soil physicochemical and microbiological properties and buckwheat yields for both soil types. Compared to BC0, the biochar addition increased buckwheat yields, on average, by 11.23% to 22.82% in aeolian sandy soil and by 7.36% to 14.87% in grey meadow soil across three years. The results of principal component analysis (PCA) and random forest analysis (RFA) indicate that soil available nutrients and microbiological properties were the most important factors influencing buckwheat yields in aeolian sandy soil and grey meadow soil, respectively. Based on RFA, the available potassium, phosphorus, and nitrogen were found to contribute at rates of 13.10%, 10.06%, and 8.12%, respectively, to buckwheat yields in aeolian sandy soil. In contrast, alkaline phosphatase, urease, and microbial biomass carbon contribute 20.26%, 8.48%, and 7.82%, respectively, to the buckwheat yields in grey meadow soil. Following biochar addition, there was greater improvement in soil health and buckwheat production for aeolian sandy soil than grey meadow soil. In conclusion, biochar addition is an effective practice for improving soil health and crop productivity in both aeolian sandy soil and grey meadow soil in semi-arid regions.