Aim Evaluate the stability of microparticles loaded with fish oil produced by spray drying, spray chilling and by the combination of these techniques (double-shell) and use the microparticles for food application. Methods Samples were stored for 180 days at 6 °C and 24 °C (75% RH). Performed investigations included encapsulation efficiency, moisture content, aw, size (laser scattering), colour (L*, a*, b*), polyunsaturated fatty acids (PUFAs) (GC), thermal behaviour (DSC) and crystalline structure (XRD). Results Double-shell microparticles containing 26 wt% core material, 22.74 ± 0.02 µm (D0.5) and 2.05 ± 0.03 span index, 1.262 ± 0.026 wt% moisture content and 0.240 ± 0.001 of aw had PUFAs retention higher than 90 wt% during storage at 6 °C without changes in crystalline structure (β’-type crystals) and melting temperature (54 °C). The sensory evaluation suggested low fish oil release in oral phase digestion. Conclusions Double-shell microparticles were effective to protect and deliver PUFAs.