Bacillus spp. are widely used in animal production for their probiotic properties. In many animal species, feed supplementation with specific Bacillus strains can provide numerous benefits including improvement in digestibility, the gut microbiota and immune modulation, and growth performance. Bacilli are fed to animals as spores that can sustain the harsh feed processing and long storage. However, the spores are metabolically quiescent and it is widely accepted that probiotics should be in a metabolically active state to perform certain probiotic functions like secretion of antimicrobial compounds and enzymes, synthesis of short chain fatty acids, and competition for essential nutrients. These functions should become active in the host gastrointestinal tract (GIT) soon after digestion of spores in order to contribute to microbiota and host metabolism. Considering that bacterial spores are metabolically dormant and many health benefits are provided by vegetative cells, it is of particular interest to discuss the life cycle of Bacillus in animal GIT. This review aims to capture the main characteristics of spores and vegetative cells and to discuss the latest knowledge in the life cycle of beneficial Bacillus in various intestinal environments. Furthermore, we review how the life cycle may influence probiotic functions of Bacillus and their benefits for human and animal health.