Bat colonies roosting in transportation infrastructure can be threatened during bridge and culvert widening, seismic retrofit, and replacement projects. Because many biologists developing mitigation for bats are not necessarily knowledgeable about bats in transportation structures or how to provide appropriate mitigation, impacts are often not adequately mitigated. This has become a conservation issue because local populations of some species depend upon bridge and culvert roosts, and are therefore at risk. After designing and implementing over 25 mitigation projects for bats in Southern California, we have developed an informal protocol for conserving bats at these structures through effective mitigation strategies. Here I discuss types of transportation projects and activities where impacts to bats may occur, and propose a systematic stepwise approach to minimizing and mitigating those impacts to bats.