The isolation of amino acid-derived metabolites from the aqueous fractions of cultures of three fungal strains is reported. From cultures of Penicillium coffeae M3 two beta-carboline alkaloids were isolated and identified, the new (+)-(1R,3R)-1-methyl-1,2,3,4-tetrahydro-beta-carboline-3-carboxylic acid (1) and the known (-)-lycoperodine-1 (2), along with the diketopiperazine cyclo[L-prolyl-L-tyrosyl] (3) and the isocoumarin 6,8-dihydroxy-3-methylisocoumarin (5). The diketopiperazines (3), cyclo[D-prolyl-L-phenylalanyl] (4) and cyclo[L-prolyl-L-phenylalanyl] (6) were isolated and identified from cultures of Trichoderma sp. L2-2. The peptaibol trichokonin VI (7) was also identified by UPLC-MS/MS analysis in aqueous fractions from cultures of the same Trichoderma sp. strain, by comparison with an authentic standard, isolated and identified from the organic fraction of the same fungus culture. The amino acid derivatives formyl-L-tryptophyl-L-alanine (8), cyclo-(D-Trp- L-Glu) (9), and (S)-Nacetyl-kynurenine (10), were isolated from cultures of the endophytic fungus Paecilomyces sp. Aa1. The planar structures of the amino acid derivatives 1-4, 6, 8-10, as well as of the isocoumarin 5, were established by analysis of spectroscopic data, including MS/MS fragmentation and comparison with literature data. The configurational assignments were performed by analysis of Marfey derivatives and/or by comparison between experimental and calculated ECD data. The results obtained give further support that investigation of aqueous fractions of fungal cultures may provide structurally relevant and potentially bioactive secondary metabolites.