Composite microgel capsules were fabricated through an ultrasonic spray accompanied by in situ surface crosslinking between glycol chitosan (GC) and benzaldehyde capped poly(ethylene glycol) (OHC–PEG–CHO) in the nebulized droplets. The methodology enables a selective one-pot encapsulation for different functional species inside the interior cavity or within the shell. Herein lithium phthalocyanine (LiPc) microcrystals and citrate stabilized iron oxide (Fe3O4) nanoparticles were selected as model materials for the functionalization, which led to the electron paramagnetic resonance (EPR) and superparamagnetic dual performance of the composite microgel capsules. This shows the potential of the microgel capsules in diagnosis and targeting delivery applications.