This work uses the fruit fly male germline as a model system to examine the manner in which a stem cell environment (niche) responds to damage, in order to maintain it’s role in regulating stem cell behavior and tissue homeostasis. We find that pathways that prevent cell death are very important in preserving niche function. In addition, we developed a system by which we can conditionally ablate (kill) niche support cells. This strategy allowed us to examine how reduction in the size of the niche leads to a concomitant loss of stem cells, providing information as to how niche size and stem cell number scales before and after damage. Therefore, our data provide important insight into the design and composition of niches built in vitro to support the maintenance and expansion of stem cells in culture.