Plant species harbor diverse rhizospheric bacteria within their resilient root zones, serving as a valuable reservoir of bioactive microorganisms with strong potential for natural antifungal and plant growth-promoting applications. This study aimed to investigate the antagonistic potential of Bacillus zhangzhouensis, isolated from Zygophyllum oxianum in the Aral Sea region, Uzbekistan, against the fungal pathogen Cytospora mali. Due to its strong antifungal activity, B. zhangzhouensis was selected for bioactive compound profiling. Methanolic extracts were fractionated via silica and Sephadex gel chromatography, followed by antifungal screening using the agar diffusion method. A highly active fraction (dichloromethane/methanol, 9:1) underwent further purification, yielding twelve antifungal sub-fractions. Mass spectrometry analysis across positive and negative ion modes identified 2475 metabolites, with polar solvents—particularly methanol—enhancing compound recovery. Refinement using Bacillus-specific references identified six known antibiotics. Four pure compounds were isolated and structurally characterized using NMR: oleanolic acid, ursolic acid, cyclo-(Pro-Ser), and uracil. Their growth regulatory activity was assessed on Amaranthus retroflexus, Nicotiana benthamiana, triticale, and Triticum aestivum at concentrations of 5, 20, 100, and 500 mg L−1. All compounds negatively affected root growth in a concentration-dependent manner, especially in monocots. Interestingly, some treatments enhanced stem growth, particularly in N. benthamiana. These findings indicate that B. zhangzhouensis produces diverse bioactive compounds with dual antifungal and plant growth-modulatory effects, highlighting its potential as a biocontrol agent and a source of natural bioactive compounds.