Calcareous soils are typically deficient in essential nutrients such as iron, phosphorus, and potassium, which frequently results in nutrient deficiency in fruit trees. Bacillus licheniformis LCDD6 markedly enhanced Malus hupehensis seedling growth and plant iron nutrition in calcareous soil. This study aimed to elucidate the mechanism underlying these beneficial effects of strain LCDD6 under iron deficiency. Transcriptomic analysis revealed that iron deficiency induced metabolic reprogramming in strain LCDD6, characterized by a significant upregulation of genes involved in the biosynthesis of the siderophore bacillibactin and plant growth hormone indoleacetic acid (IAA). Consistently, metabolomic profiling identified bacillibactin and IAA as the dominant metabolites produced under iron-deficient conditions. A 60-day pot experiment further demonstrated that the cell-free fermentation broth of strain LCDD6 significantly enhanced plant growth and rhizosphere soil enzyme activities. The crude bacillibactin extract derived from the fermentation exerted the strongest effects on plant growth and iron accumulation, whereas IAA preferentially stimulated root development and promoted plant phosphorus accumulation. Additionally, different metabolites exerted distinct and selective effects on the rhizosphere microbial community, with fungi showing stronger and more metabolite-specific responses than bacteria. The crude bacillibactin extract enriched fungal taxa, particularly Coprinellus, which showed strong positive correlations with plant growth traits and iron accumulation, while Stachybotrys, enriched under IAA treatment, was positively correlated with plant phosphorus content. Overall, strain LCDD6 promotes plant growth under iron-deficient conditions through the coordinated action of multiple metabolites, with bacillibactin as the primary contributor and IAA providing complementary effects. These findings offer mechanistic insight and a scientific basis for developing Bacillus-based biofertilizers to improve nutrient acquisition in calcareous soils.