Plant-microbiome interactions are sophisticated phenomena with unrevealed features. Current progress in RNA biology has enlightened the impact of exchanging small RNAs between plants and their associated microbes in altering the battlefield conditions in their favour. The discovery of RNAi and the release of resistant transgenic plants have raised public health concerns rushing to develop less-invasive control strategies. As an alternative, the topical application of small RNAs to inhibit gene expression via non-transformative RNAi in pathogens and pests, opens new horizons in plant disease management. The present review highlights how plants and their microbial associates send and receive small RNA molecules and that sRNAs and delivery techniques characteristics provide an effective disease control.