Obesity and its metabolic complications are associated with lower grey matter and white matter densities, whereas weight loss after bariatric surgery leads to an increase in both measures. These increases in grey and white matter density are significantly associated with post-operative weight loss and improvement of the metabolic/inflammatory profiles. While our recent studies demonstrated widespread increases in white matter density 4 and 12 months after bariatric surgery, it is not clear if these changes persist over time. The underlying mechanisms also remain unknown. In this regard, numerous studies demonstrate that the enlargement or hypertrophy of mature adipocytes, particularly in the visceral fat compartment, is an important marker of adipose tissue dysfunction and obesity-related cardiometabolic abnormalities. We aimed (i) to assess whether the increases in grey and white matter densities previously observed at 12 months are maintained 24 months after bariatric surgery; (ii) to examine the association between these structural brain changes and adiposity and metabolic markers 24 months after bariatric surgery; and (iii) to examine the association between abdominal adipocyte diameter at the time of surgery and post-surgery grey and white matter densities changes. Thirty-three participants undergoing bariatric surgery were recruited. Grey and white matter densities were assessed from T1-weighted magnetic resonance imaging scans acquired prior to and 4, 12 and 24 months post-surgery using voxel-based morphometry. Omental and subcutaneous adipose tissue samples were collected during the surgical procedure. Omental and subcutaneous adipocyte diameters were measured by microscopy of fixed adipose tissue samples. Linear mixed-effects models were performed controlling for age, sex, surgery type, initial body mass index, and initial diabetic status. The average weight loss at 24 months was 33.6 ± 7.6%. A widespread increase in white matter density was observed 24 months post-surgery mainly in the cerebellum, brainstem and corpus callosum (P < 0.05, false discovery rate) as well as some regions in grey matter density. Greater omental adipocyte diameter at the time of surgery was associated with greater changes in total white matter density at 24 months (P = 0.008). A positive trend was observed between subcutaneous adipocyte diameter at the time of surgery and changes in total white matter density at 24 months (P = 0.05). Our results show prolonged increases in grey and white matter densities up to 24 months post-bariatric surgery. Greater preoperative omental adipocyte diameter is associated with greater increases in white matter density at 24 months, suggesting that individuals with excess visceral adiposity might benefit the most from surgery.