Allelopathy is a biological process including interactions between two plants through the production of chemical compounds (allelochemicals) that are released by leaching, volatilization, decomposition, or root exudation. Hence, allelopathy together with competition is a promising environment-friendly tool especially for weed management. However, detailed knowledge of this phenomenon is necessary for its successful application due to very still limited available knowledge. Suitable use of allelopathic crops in agriculture could reduce the pesticide application and thereby reduce the environmental and food pollution, decrease costs in agriculture, improve food security in poor regions and soil productivity, and increase biodiversity and sustainability in the agro-ecosystem. Weed management in organic agriculture is one of the most difficult aspects of organic farming and uses especially preventive methods that include ways such as cover crops, mulches, green manure, and intercropping in which allelopathy could play an important role. Therefore, this review focuses on the possibilities of the allelopathy application especially in organic agriculture. Roots of allelopathic plants as cover crops, intercrops, green manure, or so-called smothering crops or decomposing residues release compounds in the soil that are toxic to weeds. The weed-suppressive effect is influenced by species, planting date, seeding rate and method, weather, and other factors. Decomposition time of plant residues and amounts of biomass are important factors of weed control by mulching. Annual, biennial, or perennial herbaceous plants in a pure or mixed stand can be grown for these purposes. Biofumigation is the name for one type of allelopathy that includes the effects of the chemicals, i.e., highly toxic isothiocyanates, produced by Brassica green manure. The balance in the crop rotation is necessary due to possible autotoxicity. These days, allelopathic plants as catch crops or trap crops found utilization in plant protection of tropical regions against parasite weeds, because they can reduce the parasite seed bank by 72%. Other applications of allelopathy for weed control include the use of plant residues as an herbicide agent, e.g., water extracts, pellets, flours, by-products of crop processing, etc. Sorgaab, an extract of sorghum, is produced commercially as a natural herbicide. Allelopathic compounds act as repellents for herbivorous pests, so the same strategy used in weed control could be effective against pests and pathogens, e.g., push–pull strategy. All possible applications of allelopathy need to combine with other methods of plant protection. Newly investigated pollen allelopathy could reduce reproductive ability of wind pollination annual weeds. Pollen of allelopathic species would be artificially dusted on the stigmatic surface of other plants. This phenomenon is yet to be studied and field tested. The new crop varieties with elevated allelopathic activity could be a great chance not only for organic farming. Hybridization could be the promising method. However, allelopathic activity was identified as a quantitative trait and therefore this characteristic is affected by both genetic effects and environmental conditions.