Parasporal crystals synthesized by Bacillus thuringiensis (Bt) have been widely used as microbial pesticides because of their toxicity to the larval stages of specific insects. However, parasporal crystals can be damaged by environmental stresses, such as high temperature, ultraviolet radiation, and desiccation. To reduce environmental susceptibility of parasporal crystals and extend the duration of their activity, we developed a new type of protection by making microcapsules of crystals (MCs). The microcapsules were self-assembled by alternate deposition (layer by layer) of low-cost chitosan and sodium alginate (or sodium carboxymethyl cellulose) on the crystal surface. Crystal toxins (Cry1Ac) were released from microcapsules at pH values above 9.0. Bioassay results demonstrated that microencapsulated preparations had larvicidal toxicity equivalent to the non-encapsulated form. Microencapsuled crystals were protected from environmental stresses such as high temperature and desiccation. The results indicate that microcapsule protection can enhance the efficacy of Bt in pest control, especially to Lepidoptera larvae that have a alkaline midgut.