In the present study, using the murine monocyte/macrophage cell line RAW264.7 as a model system, we analyzed the phagocytosis rate and the bactericidal capacity of polyunsaturated fatty acids (PUFA)-enriched macrophages against Pseudomonas aeruginosa and Rhodococcus equi. The P. aeruginosa strain ATCC 10145, the virulent R. equi strain ATCC 33701, and the non-virulent R. equi strain ATCC 6939 were examined. Flow cytometric detection of intracellular microorganisms in combination with viability assays were used to determine the impact of PUFA on the number of engulfed, surviving as well as replicating bacteria. Macrophage enrichment with PUFA resulted in an increase of the internalization rate of the microorganisms by the immune cells. Moreover, an impeding action of the unsaturated fatty acids on the intracellular survival rates of the virulent strains P. aeruginosa ATCC 10145 and R. equi ATCC 33701 could be observed. The n-3 fatty acid docosahexaenoic acid (DHA) as well as the n-6 fatty acid arachidonic acid (AA) showed the most pronounced effects. Taken together, our data support the idea of supplementing PUFA to immunocompromised individuals as well as to people suffering from chronic infections with P. aeruginosa or R. equi to improve macrophage phagocytic and microbicidal activity.