Introduction Obesity is a chronic disease associated with other comorbidities, including atherogenic dyslipidemia (AD). Bariatric surgery (BS) has shown to reduce cardiovascular risk (CVR) by achieving a significant weight reduction and improving the lipid profile. Different surgical techniques may have a different effect on the lipoprotein profile. Purpose To evaluate the lipid profile at 3 years after BS according to the surgical technique used and to determine which variables predict variation in the lipid profile at 3 years after BS. Methods Retrospective observational study of 206 patients who underwent BS between 2010 and 2019. We analyzed the variation of lipid parameters in the 3 years of follow-up according to the surgical technique, including a group analysis of patients according to whether they had dyslipidemia and whether they were treated or untreated and determined which variables predict variation in the lipid profile at 3 years after BS. Results There was a significant increase in high-density lipoprotein cholesterol (HDL-c) with sleeve gastrectomy (SG) and a significant decrease in total cholesterol (TC), LDL-cholesterol (LDL-c), non-HDL, and LDL/non-HDL with biliopancreatic diversion (BPD). Variables predicting lipid profile variation were surgical technique and pre-surgery lipoprotein level. Conclusions Malabsorptive techniques achieve a greater decrease in TC and LDL-c throughout follow-up and could also improve residual cardiovascular risk (non-HDL and LDL/non-HDL). The type of surgical technique and the presurgery lipid profile predict variation after 3 years of BS. Graphical abstract