Background Pesticides have become a central public health problem and a source of environmental contamination. The use of organic matter is an important strategy to reduce synthetic agrochemicals, improve soil conditions, and increase nutrient uptake by plants. Organic matter can also induce plant resistance against biotic stress in some circumstances. However, the results reported for different types of organic matter applications are often very different form each other, thus making difficult their interpretation and hindering and discouraging their use as valuable alternative. Identifying the main factors involved in the efficacy of these sustainable methodologies and the associated research gaps is important to increase the efficiency of organic matter and reduce the use of pesticides. Materials and methods We performed a comprehensive meta-analysis of the current recent scientific literature on the use of organic matter as control method for pest and disease, using data reduction techniques, such as principal component analysis. We found 695 articles listing the keywords in the databases between 2010 and 2021 and selected 42 that met inclusion criteria. Results In general, all organic matter reported showed a high inhibition of pests and diseases. Control effectiveness was close to 75% for fungal diseases and 67% for the pest control. The source of organic matter most frequently reported was the vermicompost. However, humic substances showed the greatest effectiveness of 74% when compared to both fungal and bacterial disease control. The concentration of humic substances ranged from 1 to 500 mg L−1, with the highest concentrations used in case of soil application. Conclusions The study demonstrated the potential role of organic matter as a resistance elicitor in plants, thus allowing a partial/total reduction of pesticides in crops. Despite the efficiency reported in the works, the mechanisms of induction of pest and disease control remains poorly studied. Graphical Abstract