Background/Aim: Roux-en-Y gastric bypass (RYGB) with a long biliopancreatic limb (BPL) was demonstrated to further improve type 2 diabetes (T2D) outcomes. Whether benefits occur at the cost of a negative impact on nutrient absorption is a matter of debate. Our aim was to evaluate the impact of RYGB BPL length on short-term nutrient absorption. Methods: Subjects (N = 20) submitted to RYGB with a 2 m BPL (n = 11) or standard BPL (60–100 cm) (n = 9) 4.2 ± 0.4 years earlier underwent a mixed meal tolerance test. Plasma metabolites were analyzed at baseline and after meal by nuclear magnetic resonance (NMR) spectroscopy. Spectra were subject to multivariate analysis (MVA). Partial least square discriminant analysis (PLS-DA) was used to identify metabolites responsible for group discrimination. Results: Principal component analysis and PLS-DA showed a clear separation between plasma metabolites before and 30 min after meal intake in both groups. The metabolites responsible for differences between time points were glucose and branched-chain amino acids. A complete overlap in metabolite species and concentrations was observed at 0 and 30 min time points for both groups, while acetate levels 120 min after the meal intake were significantly higher in subjects submitted to RYGB with a 2-m-long BPL as compared to the group submitted to the standard RYGB procedure. Conclusions: Post-prandial plasma metabolomics profiles suggest that a 2-m-long BLP RYGB does not have a negative impact on acute metabolite absorption. RYGB BPL length seems to influence post-prandial acetate levels, which could contribute to the additional positive metabolic outcomes.