Sclerotia are vegetative structures that play a major role in survival of fungi under adverse conditions. The sclerotia of the plant pathogen Rhizoctonia solani AG2-2 IIIB exude liquid brown droplets that were evaluated for their bioactivity and toxicity against microorganisms and plant species. Also, their metabolic composition was analyzed by integrating Fourier transform ion cyclotron resonance-mass spectrometry (FT-ICR/MS), gas chromatography-MS (GC/MS), and proton nuclear magnetic resonance ((1)H NMR) spectroscopy. The results showed that exudates are complex mixtures composed of phenolics (17.40%), carboxylic acids (12.79%), carbohydrates (6.08%), fatty acids (3.78%), and amino acids (3.47%). The presence of such metabolites contributed to their antifungal and phytotoxic activities. The biological interpretation of the results highly suggests that the exudates not only have multiple roles in fungal physiology but also are a potential bioactive source with moderate toxicity. Our findings show with certainty that the integration of different analytical platforms is a powerful approach for extracting the maximum and reliable information on the metabolic composition of complex biological samples.