We investigated the influence of different dietary formulation of n-3 polyunsaturated fatty acids (PUFA) on rat tissue fatty acid (FA) incorporation and consequent modulation of their bioactive metabolite N-acylethanolamines (NAE). For 10 weeks, rats were fed diets with 12% of fat from milk + 4% soybean oil and 4% of oils with different n-3 PUFA species: soybean oil as control, linseed oil rich in α-linolenic (ALA), Buglossoides arvensis oil rich in ALA and stearidonic acid (SDA), fish oil rich in eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), Nannochloropsis microalga oil rich in EPA or Schizochytrium microalga oil rich in DHA. FA and NAE profiles were determined in plasma, liver, brain and adipose tissues. Different dietary n-3 PUFA distinctively influenced tissue FA profiles and consequently NAE tissue concentrations. Interestingly, in visceral adipose tissue the levels of N-arachidonoylethanolamide (AEA) and N-docosahexaenoylethanolamide (DHEA), NAE derived from arachidonic acid (AA) and DHA, respectively, significantly correlated with NAE in plasma, and circulating DHEA levels were also correlated with those in liver and brain. Circulating NAE derived from stearic acid, stearoylethanolamide (SEA), palmitic acid and palmitoylethanolamide (PEA) correlated with their liver concentrations. Our data indicate that dietary n-3 PUFA are not all the same in terms of altering tissue FA and NAE concentrations. In addition, correlation analyses suggest that NAE levels in plasma may reflect their concentration in specific tissues. Given the receptor-mediated tissue specific metabolic role of each NAE, a personalized formulation of dietary n-3 PUFA might potentially produce tailored metabolic effects in different pathophysiological conditions.