The aim of the study was to evaluate the effect of the duration (24 hours, 60 days and 120 days) of frozen storage (−20 ºC) on the fatty acid composition of meat from ostriches supplemented with linseed and rapeseed. The study was carried out on muscles of 40 ostriches raised on five dietary groups: control with no supplementation (C), with 4% linseed (L4); 8% linseed (L8); and 5% rapeseed (R5); or 10% rapeseed (R10) in the diet. As the frozen storage period increased, the fatty acid profile of the ostrich meat in all the “enriched” groups changed, especially treatments L4 and L8. There was a decrease in the polyunsaturated fatty acid content (especially from 61 to 120 days of storage) including linolenic, arachidonic and docosahexaenoic acids. However, storage did not influence the fatty acid profile of ostrich meat up to 60 days. These results suggest that freezing is an acceptable method for preserving ostrich meat (up to 60 days), causing only a small decrease in the fatty acids of ostrich meat enriched with n-3 fatty acids. However, further research on prolonged frozen storage is recommended.