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Wastage of byproducts such as canola meal is a pressing environmental concern, and canola protein isolate (CPI)−chitosan (Ch) coacervates have a good potential to utilize and convert the wastes into a high value added product. Yet so far, there is very limited rheological and microstructural information to assist in proper utilization of CPI -Ch complex coacervates. The rheological and microstructural properties of the complex coacervates formed from CPI and chitosan Ch at various CPI-to-Ch mixing ratios (1:1, 16:1, 20:1, and 30:1) and pH values (5.0, 6.0, and 7.0) were therefore investigated. These CPI−Ch complex coacervate phases were found to exhibit elastic behavior as evidenced by significantly higher elastic modulus (Gʹ) compared to viscous modulus (G ) in all the tested ratios and pH ranges. They also exhibited shear-thinning behavior during viscous flow. The complex coacervates formed at the optimum CPI-to-Ch ratio of 16:1 and pH of 6.0 demonstrated the highest Gʹ, G , and shear viscosity, which correlated well with the high strength of electrostatic interaction and thick-walled, sponge-like, less-porous microstructure at this condition. The higher shear viscosity of the coacervate at pH 6.0 was most likely induced by stronger attractive electrostatic interactions between CPI and Ch molecules, due to the formation of a rather densely packed complex coacervate structure. Hence, it can be concluded that the microstructural observations of denser structure correlated well with the rheological findings of stronger intermolecular bonds at the optimum CPI-to-Ch ratio of 16:1 and pH of 6.0. The complex coacervate phase formed at a CPI-to-Ch ratio of 16:1 and pH of 6.0 also showed glassy consistency at low temperatures and rubbery consistency above its glass-transition temperature. This study identified the potential for the newly developed CPI-Ch complex coacervate to be used as an encapsulating material due to its favorable strength. This would drastically reduce the wastage of byproducts, provide a solution to tackle the pressing global issue of wastage of byproducts, and bring about a more environmentally friendly paradigm.