Lactobacillus plantarum A17 was encapsulated in a series of matrices of whey protein isolate (WPI) formulated with varying degrees of denaturation induced either by acid or heat treatment prior. Zeta potential measurements were used to study the complexation of WPI and the bacteria at different pH values. Whey protein capsules obtained at pH 7 (native) and 4 as well as those at pH 7 but with heat treatment at 75 C for 1 min or 78 C for 10 min showed survival rates during spray drying of 69.0, 39.3, 40.3 and 25.0% respectively. Significantly higher survival of cells was observed in the matrix of native WPI where the protein structure was more compact and globular. After exposure to acid at pH 4, the survival of A17 was reduced to ~39%. It appears that a lower degree of protein denaturation before spray drying as characterized by Micro-DSC benefits the survival of A17 during encapsulation. In addition, spray drying conditions (outlet temperature of ~70 C) did not contribute significantly to further denaturation of the WPI matrix. A unique layer-by-layer electrostatic mechanism involved in encapsu- lation of A17 at pH 7 was found responsible for higher survival of these cells.