Organic production is expected to play a major role in reducing the impact of agricultural practices on the environment. Soil is considered a major component of the organic production process, and organic practices aim at increasing its health and fertility. However, the control of soil-borne pests, particularly plant-parasitic nematodes, can be difficult in organic horticultural crops due to the rules allowed in this farming system. Applying a holistic approach that fosters and exploits the activity of the soil microbiome to control plant-parasitic nematodes has been at the basis of the analysis of the available scientific knowledge carried out for this review article. This review thus focuses on the multifunctional capacity of microorganisms, including that of bacteria and fungi not normally considered biocontrol agents, and the need to also better understand their relations with the plant and other environmental and agronomic factors. The implementation of the \u201cmulti-biotics\u201d concept, applying prebiotics, probiotics and postbiotics, which supports an integrated agroecological strategy for the protection of organic horticultural crops, is proposed as an efficient practice that should be further studied to be adapted under different crops and pedo-climatic conditions.