The fatty acid composition of broiler chicken tissues can be increased by adding omega-3 rich ingredients to their diets. The purpose of this study was to compare the levels of tissue enrichment observed following the supplementation of broilers with the docosahexaenoic acid (DHA)-rich protist, Aurantiochytrium limacinum (AURA) for their whole life (42 days) or for the final 21-day fattening period. Day-old chicks (n = 350) were distributed among 35 pens (10 birds per pen) with each pen randomly assigned to one of five treatments: Control; 0.5% AURA from day 0–42; 1% AURA from day 0–42; 0.5% AURA from day 21–42; 1% AURA from day 21–42. Production parameters were recorded over the course of the study and the fatty acid profile of the breast, thigh, liver, kidney and skin with adhering fat was quantified at the end of the feeding period. The level of supplementation had a significant impact on the degree of omega-3 tissue enrichment, however, no differences were observed when the same dose was provided for 21 or 42 days. These results indicate that supplementation with AURA for a period of 21 days does not negatively affect broiler productivity and is the most efficient strategy to increase the nutritional value of broiler products.