The benefits of active learning have been repeatedly demonstrated in educational research from the last few decades. One way to bring active learning into classrooms is to have students work on challenging problems during the class period. We present a collection of microbiology problems on various topics (including evolution, cell structure, metabolism, genetics, ecology, and pathogenesis) that we have used as in-class activities in a large microbiology lecture. We present this as a tool for teachers to encourage the use of active learning. These activities will give students a better understanding of the concepts and will help them to enjoy the lecture experience.