Bioactive compounds in algae, have chain rings that protect the tissue from chemical damage and disease symptoms. In addition, algal bioactive agents have the ability to stimulate the immune system, protective and therapeutic effects against many diseases, including various types of cancers, coronary heart disease, premature aging and arthritis. These bioactive compounds have also antioxidant, anticoagulant, antiviral and anti-inflammatory properties. It is very important to encapsulate these algal compounds for preserving bioactive properties. Two of the most efficient methods used for encapsulation are electrospraying and microemulsion techniques. While electrospraying is a novel technique to produce nanoparticles in recent years, microemulsion is more conventional method compared to electrospraying. In this study, Chlorella protothecoides oil was encapsulated by using sodium alginate and chitosan biopolymers, and the effects of production parameters of electrospraying and microemulsion methods on the particle size and loading efficiency were investigated. Statistical modelling of critical parameters for particle sizing in microemulsion method and electrospraying technique which is a novel approach to obtain microalgal oil loaded nanoparticles was also presented. It was seen that electrospraying is suitable for obtaining smaller nanoparticles (123.9-610 nm), homogeneous distribution and higher oil loading efficiency (60-77 %) compared to microemulsion method (756.9-1128.2 nm and 57-73%). This article is protected by copyright. All rights reserved.This article is protected by copyright. All rights reserved.