Iron (Fe) deficiency is a common abiotic stress on plants growing in calcareous soils where low organic matter content, high carbonate–bicarbonate concentration, and high pH precipitate Fe in unavailable forms. Enzymatic activity is a mechanism for plants to access soil nutrients; enzymes such as H+-ATPase, phosphoenolpyruvate carboxylase (PEPC), and the intracellular enzyme ferric reduction oxidase (FRO) are involved in Fe absorption. The effects of the application of citric acid (CA) and humic-like substances (HLS) on the yield, H+-ATPase, PEPC, and FRO enzyme activity, and expression of LeHA1, LePEPC1, and LeFRO1 genes in tomato plants grown under calcareous soil were studied. CA and HLS improved the SPAD units and increased the number of harvested fruits and yield per plant. Temporary alterations in enzyme activity, which reduced PEPC and FRO activity in roots, were documented. In leaf tissue, CA resulted in lower expression of LeHA1 and LePEPC1 and the induction of LeFRO1 expression, whereas HLS application resulted in higher expression of LePEPC1 and LeFRO1. In roots, LeHA1 expression increased with HLS, whereas LePEPC1 and LeFRO1 showed lower expression with CA and HLS, respectively. The application of CA and HLS through a nutrient solution in combination with Fe-chelate can improve Fe nutrition in tomato plants potted in calcareous soil by inducing temporal alterations in PEPC and FRO enzyme activity and LeFRO1 and LeHA1 gene expression.