Aims: To assess the applicability of starch- and lipid-based encapsulation methods for improving the viability and culturability of two Bifidobacterium longum strains stored in fermented and nonfermented foods. Materials and Results: Cells were encapsulated with partially hydrolysed potato starch granules combined with amylose coating, or entrapped in cocoa butter matrix. The tested B. longum strains were not adherent to the starch granules, and the culturability of the cells stored in fermented and nonfermented foods was not improved by starch-based encapsulation. Encapsulation of the cells in cocoa butter was found to increase the plate counts during storage. In addition to plate counts, viability of the cells was measured by fluorescent microscopy using LIVE/DEAD BacLight viability assay. Microscopic counts of the viable cells did not change significantly during storage, suggesting that the cells remained alive despite becoming unable to grow on nutrient agar plates. Conclusions: Encapsulation with cocoa butter increased the culturability of the cells, but encapsulation with hydrolysed potato starch had no effect. Culture-independent viability assay suggested that cells remained viable despite being unable to grow on agar plates. Significance and the Impact of the Study: This study indicates that encapsulation techniques may be useful in improving the culturability of bacteria, but the plate counts may yield insufficient data on the actual viability of the cells.