Microencapsulation improves oxidative stability and shelf life of fish oil. Spray and freeze drying are widely used to produce microcapsules. Newer spray-nozzles utilize multiple fluid channels allowing for mixing of wall and core materials at the point of atomization. Sonic energy has also been employed as a means of atomization. The objective of this study was to examine the effect of nozzle type and design on fish oil encapsulation efficiency and microcapsule properties. A total of 3 nozzle types, a pressure nozzle with 1 liquid channel, a pressure nozzle with 2 liquid channels, and a sonic atomizer with 2 liquid channels were examined for their suitability to encapsulate fish oil in whey protein isolate. Physical and chemical properties of freeze dried microcapsules were compared to those of microcapsules produced by spray drying. The 2-fluid pressure and ultrasonic nozzles had the highest (91.6%) and the lowest microencapsulation efficiencies (76%), respectively. There was no significant difference in bulk density of microcapsules produced by ultrasonic and 3-fluid pressure nozzles. The ultrasonic nozzle showed a significantly narrower particle size distribution than the other nozzles. This study demonstrated that new nozzle designs that eliminate emulsion preparation prior to spray drying can be beneficial for microencapsulation applications. However, there is still a need for research to improve microencapsulation efficiency of multiple channel spray nozzles. Practical Application: Since this research evaluates new spray nozzle designs for oil microencapsulation, the information presented in this article could be an interest to fish oil producers and food industry.