Instability, leakage and unwanted release of bioactive compounds loaded into nanoliposomes (NLs) are among the key challenges during storage, formulation, or various tensions (mechanical, thermal, shear, etc.). In this study, lipid membrane stabilization of phycocyanin (PC)-containing NLs was performed through chitosan-alginate (NAs) bilayer coating. Then, the reconstitution capability and retention of the biological properties of nanoproliposomes (NPLs) was investigated. The polymer complex led to improved nanovesicle properties (216 nm, −33.6 mV), encapsulation efficiency (EE 78.2 %), physical stability, EE-retention, bioactive contents (PC and TPC), biological activities (DPPH∗/ABTS∗ scavenging), and morphology (SEM), during different tensions (thermal, light and freezing) as well as controlled release (under gastrointestinal conditions). The properties of NPLs (production yield (48–62 %), flowability (relative cohesion and compressibility), functional indices (solubility ∼93 %), hygroscopicity, retention of bioactives (∼86–96 %), histogram and color indices) were affected by the composition and type of coating. Chemical (FTIR) and thermal (DSC) evaluations indicated electrostatic adsorption of biopolymers and increased rigidity of the coated membrane. The transformation of brittle structures (FD-B-NLs) into compact and rough (FD-NAs) was confirmed by SEM images. NPLs showed particles (∼430–590 nm) with wrinkled, indented structures and intact walls. The polymer bilayer coating resulted in maintaining membrane strength, structural stability, reduced unwanted leakage (75–82 % of the initial EE), and particle morphological changes during shear/dehydration stresses after reconstitution. The findings of this study can be used to design powder formulations containing stable pharmaceutical and food nanocarriers.