Due to the upcoming enormous global food demand and overexploitation of cultivable land resources, agriculture relies increasingly on chemical fertilizers to produce more food per unit area. However, excessive and indiscriminate agrochemical use reduces soil fertility and damages beneficial soil microbial populations. Over recent years, fly ash (FA) soil supplements derived from coal processing wastes have gained momentum in agriculture in many countries worldwide, promising sustained productivity and environmental preservation. Some prospective approaches may include modifying FA with bioavailable/bioactive molecules to enhance and regulate its benefits. One such compound is humic acid (HA), a multifunctional amorphous biopolymer that can be used to improve soil properties. In this study, we performed a modification of FA with low-rank coal-derived HA and evaluated its adsorption/desorption parameters at different pH and for different incubation times. Administration of the obtained HA-FA composite to test soil in controlled pot experiments improved its physicochemical and biological characteristics measured after 60 days of treatment. Furthermore, HA-FA amendment positively correlated with the physiological diversity of the soil microbial community and the activity of polyphenol oxidase and dehydrogenase. The results suggest that the HA-FA composite has an overall positive impact on the soil quality and may beneficially contribute to current and future sustainable soil management practices.