Pathogen-specific CD4 T cells undergo dynamic expansion and contraction during infection, ultimately generating memory clones that shape the subsequent immune responses. However, the influence of distinct tissue environments on the differentiation and clonal selection of polyclonal T cells remains unclear, primarily because of the technical challenges in tracking these cells in vivo. To address this question, we generated Tracking Recently Activated Cell Kinetics (TRACK) mice, a dual-recombinase fate-mapping system that enables precise spatial and temporal labeling of recently activated CD4 T cells. Using TRACK mice during influenza infection, we observed organ-specific clonal selection and transcriptional differentiation in the lungs, mediastinal lymph nodes (medLNs), and spleen. T cell receptor (TCR) sequencing revealed that local antigenic landscapes and clonal identity shape repertoire diversity, resulting in a low clonal overlap between tissues during acute infection. During the effector phase, spleen-derived CD4 T cells preferentially adopted a stem-like migratory phenotype, whereas those activated in the medLNs predominantly differentiated into T follicular helper (Tfh) cells. Memory formation was associated with increased clonal overlap between lung and medLN-derived cells, whereas splenic clones retained a distinct repertoire. Additionally, memory CD4 T cells displayed converging antigen specificity across tissues over time. These results highlight the tissue-dependent mechanisms driving clonal selection and functional specialization during infection and underscore how memory development facilitates clonal redistribution and functional convergence.