Significance Germinal centers (GCs) are critical for the generation of memory B cells and high-affinity antibody-producing cells. This process is important for protection from acute infections and for establishment of long-lasting immunity in response to vaccination. The microanatomic organization of distinct niches within lymphoid tissues is fundamental for GC responses, as it provides the basis for coordinated interactions between rare antigen-specific cells and antigen-presenting cells. Here we reveal a role for a specialized resident macrophage subset in maintaining positional regulation of a key antigen-presenting cell type within functional niches in the spleen. Our study demonstrates the importance of this regulation to humoral immunity.