In this study, the efficacy of chitosan (C)/pectin (P) complexes on physical properties, stability, retention of bioactive compounds (phycocyanin (PC) and total phenolic compounds (TPC)) and antioxidant activity (AA), morphology, encapsulation efficiency (EE), chemical structure, and release of PC-loaded nanovesicles (NLs/NCs/NPs) during heat, Freeze-thaw (F-T), light, and digestive stresses were investigated. Finally, the jelly was fortified with free and NLs-PC and the color indices, histograms, and sensory parameters were evaluated. Successful coating of NLs was confirmed through electrostatic reactions, hydrogen bonds (H-bonds) formation, and ionic complexes (FTIR). The secondary coating (NPs) led to increased membrane compactness, stiffness, and resistance to thermal and light stresses. Morphological and structural characteristics of the system (SEM, TEM and AFM) were preserved. Also, instability mechanisms (aggregation, agglomeration and membrane rupture), leakage and unwanted release of loaded PC were minimized. On the other hand, a significant portion of PC (74–89 %), TPC (78–93 %), and AA (88–96 %) were retained in NPs during the mentioned stresses. Protection of the membrane (C-P coating) against acidic conditions (stomach) and lipolysis (intestine) resulted in controlled release and improved bioavailability. PC-containing nanovesicles (NLs/NCs/NPs) changed the histogram, maintained the natural color (especially NLs), sensory indices, and masked the undesirable PC taste in fortified jellies. The results of this study can be considered to improve the delivery and bioavailability of PC (as a bioactive and natural pigment) in food, pharmaceutical, and cosmetic formulations.