In the present work, we aimed to explore the molecular binding between alginate and β-galactosidase, as well as the effect of this interaction on the activity retention, thermal stability, and kinetic properties of the enzyme. The impact of pH and enzyme/alginate ratio on physicochemical properties (turbidity, morphology, particle size distribution, ζ-potential, FTIR, and isothermal titration calorimetry) was also evaluated. The ratio of biopolymers and pH of the system directly affected the critical pH of complex formation; however, a low alginate concentration (0.1 wt%) could achieve an electrical charge equivalence at pH 3.4 with 93.72% of yield. The binding between β-galactosidase and alginate was an equilibrium between enthalpic and entropic contributions, which promoted changes in the structure of the enzyme. Nevertheless, this conformational modification was reversible after the dissociation of the complex, which allowed the enzyme to regain its activity. These findings will likely broaden functional applications of enzyme immobilization.