Spray drying can be used to manufacture powder ingredients with lactic acid bacteria. Carrier matrices are used to increase survival of bacteria during drying; however, it is not exactly known why some matrices provide better protection than others. Depending on the carrier matrix and the drying conditions, different powder particle morphologies are obtained. Here, we employed single droplet drying to investigate the relation between particle morphology and survival of Lactobacillus plantarum WCFS1. Different carrier matrices with varying physicochemical properties were selected and dried at 90 °C (R0~100 μm), yielding smooth, hollow or dented morphologies. A clear correlation was observed between the observed particle morphologies and the viabilities after drying. Highest survival (78–90%) was obtained for dense and smooth particles; low survival (2–8%) was obtained for dented particles. The relation between the morphology and survival is likely to be rooted in a complex interplay between matrix properties and dynamics, where a skin that hinders evaporation most resulted in the highest inactivation. The identified correlation between morphology development and bacterial survival will be important to identify the mechanisms of inactivation of bacteria during drying.