Obesity and overweight are strongly associated with dyslipidemia which can promote the development of cardiovascular diseases. Recently, natural products have been suggested as alternative compounds for antioxidant and antilipidemic activity. The objective of this study was to determine the phenolic compounds and assess the inhibitory activities on pancreatic lipase, cholesterol esterase, and cholesterol micellization of nipa palm vinegar (NPV). Total phenolic content was assessed and phenolic compounds were determined using the Folin–Ciocalteu assay and liquid chromatography-mass spectrometry (LC-MS), respectively. Pancreatic lipase and cholesterol esterase inhibitory activities of the NPV were measured using enzymatic colorimetric assays. The formation of cholesterol micelles was assessed using a cholesterol assay kit. The phenolic content of NPV was 167.10 ± 10.15 µg GAE/mL, and LC-MS analyses indicated the presence of gallic acid, isoquercetin, quercetin, catechin, and rutin as bioactive compounds. Additionally, the NPV inhibited pancreatic lipase and cholesterol esterase activities in a concentration-dependent manner. Moreover, the NPV also suppressed the formation of cholesterol micellization. These results suggest that phenolic compounds, especially gallic acid, isoquercetin, quercetin, catechin, and rutin, from NPV may be the main active compounds with possible cholesterol-lowering effects through inhibition of pancreatic lipase and cholesterol esterase activities as well as the inhibition of solubility of cholesterol micelles. Therefore, NPV may delay postprandial dyslipidemia, and it could be used as a natural source of bioactive compounds with antilipidemic activity. However, NPV should be extensively evaluated by animal and clinical human studies.