Purpose of review: This article summarizes the recent literature concerning vitamin deficiency and required supplementation post bariatric surgery (BS), with a focus on vitamin (and associated clinical adverse effect on bone loss) and on the potential implication of the gut microbiota. Recent findings: BS improves health outcomes in terms of weight loss and metabolic alterations yet with major inter-individual variability. Indeed, although BS is efficient in most patients, some display poor response (i.e. patients with the lowest weight loss at one year or weight regain afterwards, or patients who do not undergo metabolic disease remission). Furthermore, despite systematic vitamin supplementation post-BS, some patients develop vitamin deficiencies leading to poor clinical outcomes. Specifically, a major recently described adverse outcome is vitamin D deficiency associated in part with observed bone mass loss and fractures. Recent mechanistic studies have been performed to better understand the involved physiopathology. Furthermore, different intervention studies tested on top of BS (using vitamin supplementation, diet or nutrients acting as functional food) have evaluated whether they could improve these nutritional adverse outcomes and are summarized herein. Importantly, gut microbiota involved in food digestion and metabolization as well as vitamin synthesis, is largely perturbed during severe obesity and is partially restored post-BS, yet again with large inter-individual variability. Whether differential modification of the gut microbiota could be associated with those vitamin deficiencies is an open question. Summary: Future clinical research studies will need to evaluate whether add-on intervention to BS using vitamin, diet or specific food items could help prevent nutritional deficiencies and improve clinical response observed post-BS. More importantly, personalizing the add-on intervention after BS upon gut microbiota composition should be tested in predicted poor responders to BS as already performed during diet intervention to further improve metabolic health.