This study sheds light on the influence of fluoride on the changes in the properties of alkaline sandy soils and the efficiency of calcium-enriched biochar application. The investigation involved an incubation experiment with soil contaminated with varying NaF concentrations (0, 400, 800, and 1200 mg NaF kg-1 soil) and biochar (1% w/w). The data revealed that adding NaF to the soil resulted in significant increases in soil pH and decreases in total nitrogen (TN) content. Short-term fluoride pollution did not affect the microbial abundance due to certain factors such as increased soil pH and decreased microbial metabolism promoting the survival of cells under fluoride stress. However, a shift from bacterial to fungal-dominated microbial communities was observed at the highest NaF concentration. The nitrogen functional gene amoA was found to be highly sensitive to fluoride toxicity. The decrease in the abundance of amoA gene and the increase in soil pH can explain reduced nitrogen concentration. On the other hand, our findings indicated a significant decrease in enzyme activity in soil contaminated with mild to severe levels of NaF. This reduction in enzyme activity can be attributed to increased soil pH, decreased TN content, and the inhibition of microbial metabolism due to fluoride toxicity. Furthermore, the addition of calcium-rich biochar reduced fluoride solubility and adjusted pH, mitigating the negative effects of fluoride toxicity on soil properties. The use of biochar was also found to inhibit the accumulation of soil fluoride-resistant microbial genes.