Metabolites are organic molecules produced by metabolic processes in living organisms and are responsible for various cellular functions. They are obtained from both terrestrial and marine organisms. Among marine organisms, sponges are an important source of metabolites. Clathria reinwardti Vosmaer is a demosponge belonging to the order Poecilosclerida and the family Microcionidae. The study aims to profile the metabolites of the chloroform extract of the marine sponge C. reinwardti using mass spectrometry analysis. A sponge sample was collected from the east coast of Sulug Island, Sabah, Malaysia. Total phenolic and flavonoid contents were determined. The composition of these extracts was further elucidated through qualitative biochemical screening, Fourier transform infrared spectroscopy (FTIR), gas chromatography-mass spectrometry (GC-MS), and liquid chromatography-quadrupole time-of-flight mass spectrometry (LT-qTOF-MS) analyses. The extracts displayed total phenolic and flavonoid content values. The qualitative biochemical screening tests indicated the presence of alkaloids and steroids. The GC-MS analysis indicated the presence of different metabolites of various natures, which include 2,5-bis(1,1-dimethylethyl) phenol, pentadecane, octacosane, eicosane, tetracosane, and cholestanol. The LC-qTOF-MS analysis indicated the presence of thymine, C16 sphinganine, hericene B, phylloquinone, 24-norcholesterol, palmitic amide, oleamide, solanidine, suillin, 9-thiastearic acid, and isoamijiol. The detected metabolites have been reported to have different pharmacological activities such as anti-inflammatory, antimicrobial, anti-diabetic, anti-cancer, antioxidant, anti-haemorrhagic, cytotoxic, neuroprotective, and chemopreventive. The finding highlights that the chloroform extract of C. reinhardt is an important source of metabolites with potential benefits to humans and animals, particularly in the aquaculture industry. Further isolation, purification, and characterization of the detected metabolites are needed for future studies.