The excessive use of synthetic chemicals in agriculture demands sustainable alternatives to combat crop-affecting microorganisms. Plant-derived secondary metabolites have garnered attention as promising candidates with antimicrobial properties. This study investigates the antimicrobial potential of tobacco plants, specifically non-commercial accessions Nic 1015 (“TI 1341”) and BHmN, recognized for their rich bioactive compounds. Our objectives encompassed the extraction of leaf surface compounds and the assessment of their in vitro antimicrobial activity against crop-damaging microorganisms. Ethanol-based extracts, abundant in diterpenes, were meticulously analyzed. Notably, BHmN contained cis-abienol, while both accessions featured α-CBT diol, as confirmed by thin-layer chromatography (TLC) and high-performance liquid chromatography (HPLC). TLC-Bioautography and microdilution assays unveiled substantial antifungal activity. The growth inhibition percentages correlated with extract concentrations, highlighting the pivotal role of diterpenes. These extracts exhibited pronounced efficacy against Rhizoctonia solani and Stemphylium solani but displayed relatively weaker activity against Sarocladium oryzae. Notably, Nic 1015 extract demonstrated remarkable antifungal activity at a minimal concentration of 78 µg·mL−1, while cis-abienol and sclareol inhibited the growth of Fusarium graminearum and Alternaria alternata. Additionally, the extracts demonstrated in vitro antibacterial activity against common plant culture contaminants, Bacillus licheniformis and Stenotrophomonas maltophilia. In conclusion, the findings underscore the potential of these extracts as effective tools for controlling pathogenic fungi and bacterial contaminants in plant in vitro cultures. Harnessing plant-derived secondary metabolites, especially those from tobacco leaf surface, presents a sustainable and eco-friendly strategy to mitigate the detrimental impact of microorganisms on agricultural crops, promising a greener alternative to synthetic chemical products.