Changes in fatty acid composition of longissimus muscle and subcutaneous adipose tissue of German Holstein bulls induced by a grass-silage/n-3 fatty acid based intervention diet versus a maize-silage/n-6 fatty acid based control diet were analyzed and related to shifts in lipogenic gene expression, protein expression, and enzyme activity patterns. Significantly higher amounts of n-3 fatty acids and by mean factors of 2.2-2.5 decreased n-6/n-3 fatty acid ratios in both tissues were obtained upon n-3 fatty acid intervention. In longissimus muscle, these changes of fatty acid profiles were associated with reduced SREBP1c (p = 0.02), ACC (p = 0.00), FAS (p = 0.10) and SCD (p = 0.03) gene expression, Δ6D (p = 0.03) and SCD (p = 0.03) protein expression as well as SCD enzyme activity (p = 0.03). In subcutaneous adipose tissue, significantly reduced ACC (p = 0.00) and FAS (p = 0.01) gene expression, SCD protein expression (p = 0.02) and SCD enzyme activity (p = 0.03) were detected upon n-3 fatty acid intervention, although lower degrees of correlation between gene and corresponding gene products were obtained in relation to longissimus muscle. The study elucidates tissue-specific functional genomic responses to dietary fatty acid manipulation in regard to fatty acid profile tailoring of animal tissues.