Bariatric surgery has helped patients attain not only significant and sustained weight loss but has also proved to be an effective means of mitigating or reversing various obesity-related comorbidities. The impressive rates of remission or resolution of type 2 diabetes mellitus (T2D) following bariatric surgery are well documented and have rightly received great attention. Less understood are the effects of bariatric surgery on cardiovascular disease (CVD) and its underlying risk factors. Thanks to the availability of increasingly sensitive laboratory tools, the emerging science of lipidomics and metagenomics is poised to offer significant contributions to our understanding of metabolically induced vascular diseases. They are set to identify novel mechanisms explaining how the varied approaches of bariatric surgery produce the remarkable improvements in multiple organs observed during patient follow-up. This article reviews recent and novel findings in patients through the lens of lipidomics with an emphasis on CVD.