Enduring protection from invading pathogens depends on generation of long-lived memory and antibody-secreting cells in germinal centers (GC). Here, we map the positions of all the activated single B cells and GC-departing cells in the context of an intact lymph-node throughout the immune response. By combining light-sheet fluorescence-microscopy with reporter mice, we find that most of the single B cells that expressed AID including GC-departing cells, primarily localize to the lymph-node cortex and do not show typical memory or plasma cell markers. Analysis of the entire structure of individual GCs and in-situ photoactivation experiments demonstrate that B cells depart primarily through the GC area that encompasses the light-zone. Mechanistically, we find that B cell-receptor affinity plays a more significant role in GC-departure than in GC-seeding. Thus, whole-organ imaging captured single-cell dissemination patterns in the context of an intact organ, and revealed the path taken by B cells during the GC-reaction.