Encapsulated microbial compositions with increased stability, which, for example, can be applied to a plant seed to promote growth and/or provide pest control, and methods for preparing such encapsulated microbial compositions with increased stability are described. The method can include combining a microbe and at least one hydrogel, such as an alginate, to form a precursor mixture, solidifying the precursor mixture with a cross-linking agent including a divalent cation, a divalent cation salt, or a combination thereof to form an intermediate microbial composition, and drying the intermediate microbial composition to form the encapsulated microbial composition.