Recent shift in preference of biological products over chemical seed treatments has resulted in an increased requirement for development of formulations to improve viability and consistency of microbial inoculants. Two of the biggest challenges in introducing biological products to the agriculture industry are stability of formulations and compatibility with common agriculture chemicals. In this study, multiple alginate encapsulation formulations were examined to not only increase shelf stability of microbes but also to improve their protection from various environmental factors. The initial alginate formulation extended stability of sensitive organisms to one year for both on shelf and on seed. The addition of a hydrophobic coating to the formulation protected cells from agriculture chemicals permitting at least three months of survival on shelf and on seed, with little to no viability loss after chemical exposure, in comparison to free microbials. This improved formulation is scalable for field application and provides a new platform for increased viability of agriculturally relevant microorganisms.