This work was proposed to prepare multi-functional omega-3 oil based microcapsules. Rosemary (Rosmarinus officianlis L.) extracts as potential active compounds were used to stabilize these omega-3 rich microcapsules against both oxidation and microbes. Solvents of different polarities as well as ultrasonic-assisted water extraction (UAE) technique were tested for preparing promising extracts. Results demonstrated that water extract showed the highest phenolic extract as well as highest radical scavenging activity (RSA %) even when compared with BHT as a reference synthetic antioxidant. However, the potency of ultrasonic-assisted water extract as a radical scavenger was greatly enhanced specifically at a temperature of 45C and 30 min extraction time. Regarding the antimicrobial activity, although giving highest total phenolics and RSA %, water extract had no antimicrobial activity against both Gram negative or Gram positive bacteria (at concentration range 0.25 –15 %) while methanol extract revealed inhibitory activity against all tested pathogens at concentration of 5 % or higher. Moreover, methanol extract didn't affect the survivability of the beneficial bacteria of lactobacilli strains. Finally, according to the results the microcapsules prepared by spray drying method exhibited better protection of omega-3 rich oils and also the yogurt fortified with spray-dried fish oil capsules had higher score in sensory evaluation.