The effect and mechanisms of calcium chloride and citric acid addition on the acid method of processing tilapia protein isolates and surimi gels were studied. The alkaline method shows better gel quality than the acid method with lower yield and high lipid content. The addition of calcium chloride increased the breaking force to 494.56 g and citric acid helped reducing the lipid content by 85.85%, resulting in a higher yield of 75.36%. Gels with calcium maintained low levels of expressible moisture (2.30%), indicating a well-organised gel matrix. The decrease in -SH content and increase in ionic bonds content suggested increased formation of disulphide bonds and ionic bonds. Oscillatory dynamic measurement indicated that more heat resistant bonds were formed. The morphology of myofibril proteins studied by atomic force microscopy (AFM) showed that the height of the proteins in the calcium-added gels decreased 79.4%, which suggested that the protein structure was “suppressed”.