The use of humic acids in agricultural production worldwide dates back several decades and numerous scientific studies support the beneficial effects of the compounds. However, less information is available about their combined use with macro- and microelements. The aim of our study was to investigate the effects of humic acids combined with boron and sulfur using modern genetic tools. We performed genome-level transcriptomic analyses using the Next Generation Sequencing (NGS) technique and found that the combined use of humic acids with nutrients positively influences several plant biochemical processes. Its beneficial effects extend to certain stages of photosynthesis and cellular respiration, and also affect the function of some ribosomal genes. However, among the findings previously published in the literature, at the gene level we were unable to confirm additional positive effects (e.g. stress-relieving, antioxidant effects, etc.) that can be derived from the individual or combined use of humic acids. Our studies provide deeper insight and explain the transcriptomic background of changes in some plant physiological processes observed upon application of humic acid solutions.