Changes in the lipid oxidation and volatile compounds of a variety of tilapia tissues (Oreochromis niloticus) including the muscle, gills, and skin during ice storage were investigated by evaluating peroxide values (PVs), lipoxygenase (LOX) activity, fatty acid (FA) composition, and volatile substances. LOX activity and PV were determined in the gills, skin, and muscles throughout 9 days of storage in ascending order to the extended storage time. The highest level of LOX activity was found in the gills, whereas the highest PV was determined in the skin. FA content of all tissues decreased during the storage period. Oleic acid was the predominant monounsaturated fatty acid, whereas linoleic acid and docosahexaenoic acid were the main polyunsaturated fatty acids and omega‐3 in all tissues. The fish gills were shown to have the highest level of volatile compounds followed by the skin and muscle, based on headspace solid‐phase microextraction coupled with gas chromatography and mass spectrometry. Principal component analysis indicated gradual changes in the volatile compound composition with increasing storage time. 2‐Butanone and nonanal in the muscle, 6‐methyl‐2‐heptanone and 2‐nonenal in the gills, and 1‐heptanol, and 1‐nonanol in the skin were found to be the potential freshness indicators. In addition, hexanal could be a general potential marker for measuring the degree of lipid oxidation in all tissues.Practical ApplicationUnderstanding the volatile compound formation related to lipid oxidation within storage time at various tissues of tilapia could be critical to the side‐stream processing to yield the desired quality.