Representatives of the genus Bacillus have been established as one of the most important industrial microorganisms in the last few decades. Genetically modified B. subtilis and, to a lesser extent, B. licheniformis, B. amyloliquefaciens, and B. megaterium have been used for the heterologous expression of numerous proteins (enzymes, vaccine components, growth factors), platform chemicals, and other organic compounds of industrial importance. Vectors designed to work in Bacillus spp. have dramatically increased in number and complexity. Today, they provide opportunities for genetic manipulation on every level, from point mutations to systems biology, that were impossible even ten years ago. The present review aims to describe concisely the latest developments in the shuttle, integrative, and CRISPR-Cas9 vectors in Bacillus spp. as well as their application for large-scale bioengineering with the prospect of producing valuable compounds on an industrial scale. Genetic manipulations of promoters and vectors, together with their impact on secretory and metabolic pathways, are discussed in detail.