Trachoma, caused by Chlamydia trachomatis (Ct), remains a leading cause of preventable infection-induced blindness worldwide. We conducted a 4-year longitudinal study in three trachoma-endemic villages in Northern Tanzania, tracking infection dynamics and factors influencing trachomatous scarring progression and persistence pre- and post-mass drug administration (MDA) interventions. We analysed 118 whole genomes of Ct originating from ocular swabs of children. Sample collection was conducted at 3-month intervals over 4 years, encompassing 15 timepoints. We studied Ct phylogeny and patterns of SNP accumulation within sequences in the Ct genotype A (CtA) and Ct genotype B (CtB) phylogenetic clades, with the association of clinical signs of trachoma and scarring progression. Of the samples analysed, 71 (60.2%) were identified as CtA and 47 (39.8%) as CtB. We observed a significant shift in genotype prevalence: CtB predominated in pre-MDA samples (36 out of 40, 90%), whilst CtA became the dominant genotype after the first MDA round (67 out of 78, 85.9%) (P<0.0001). Phylogenetic analysis revealed two distinct CtA clades: clade 1 (29 sequences) was primarily found pre-MDA and shared a common ancestor with Tanzanian CtA reference genomes, whilst clade 2 (42 sequences) emerged post-MDA and exhibited a characteristic ~6 kbp reduction in the plasticity zone (PZ). Similarly, CtB sequences formed two distinct clades, both sharing ancestry with a Tanzanian CtB reference genome. Notably, we identified variable genome reduction in the PZ (~4 and ~10 kbp) amongst 13 CtB sequences distributed across both clades. We documented a significant shift in Ct genotype distribution following the first round of MDA, characterized by the emergence of CtA strains with distinct genetic profiles compared to pre-MDA strains. The observed reductions in Ct genome size suggest ongoing evolutionary processes shaping these bacterial populations. Additional research is needed to understand the dynamic changes in Ct lineage composition before and after antibiotic interventions and to determine how variations in genome size influence Ct biology and its susceptibility to azithromycin treatment.