Marine organisms have evolved to survive against predators in complex marine ecosystems via the production of chemical compounds. Soft corals (Cnidaria, Anthozoa, Octocorallia) are an important source of chemically diverse metabolites with a broad spectrum of biological activities. Herein, we perform a comparative study between high-resolution proton nuclear magnetic resonance (1H-NMR) and pure shift yielded by chirp excitation (PSYCHE) experiments to analyze the metabolic profile of 24 soft corals from the Colombian Caribbean to correlate chemical fingerprints with their cytotoxic activity against three cancer cell lines (human cervical carcinoma (SiHa), human prostatic carcinoma (PC3) and human lung adenocarcinoma (A549)). All data obtained were explored using multivariate analysis using principal components analysis (PCA) and orthogonal partial least squares (OPLS) analysis. The results did not show a significant correlation between clusters using 1H-NMR data in the PCA and OPLS-DA models and therefore did not provide conclusive evidence; on the other hand, a metabolomic analysis of PSYCHE data obtained under the same parameters revealed that when a decoupled experiment is performed, it was possible to establish a statistically valid correlation between the chemical composition of soft corals and their cytotoxic activity against the PC3 cancer cell line, where the asperdiol and plexaurolone markers were putatively identified and related to the cytotoxic activity presented by extracts of Plexaurella sp. and Plexaura kukenthali, respectively. These results increase the speed, effectiveness and reliability of analyses for the study of this type of complex matrices.