Background Most patients achieve successful weight loss following metabolic bariatric surgery (MBS), but they face an increased risk of micronutrient deficiencies due to altered gastrointestinal physiology and dietary restrictions. This study evaluated the impact of a specialized multivitamin on blood serum levels before MBS. Methods A prospective, within-patient comparison trial was conducted between January and July 2023 at a large bariatric clinic. Differences in serum micronutrient levels between baseline and the 3-month follow-up were assessed, along with changes in the prevalence of micronutrient deficiencies. Results Of 120 patients recruited, 99 (82.5%) completed the 3-month follow-up. Significant changes were observed in 13 of 21 serum parameters (61.9%). Ten parameters, including iron, vitamin K1, zinc, C-reactive protein, hemoglobin, hematocrit, mean corpuscular volume, calcium, folic acid, and vitamin D, showed significant increases (p < 0.001). Conversely, magnesium, phosphate, and albumin levels significantly decreased (p < 0.001). Among 21 parameters, deficiencies were identified in 17 (80.1%), with prevalence rates ranging from 1.0% (copper) to 88.8% (vitamin D). After 3 months, significant reductions in deficiency prevalence were observed for iron, folic acid, and vitamin D. However, phosphate deficiency increased significantly, from 2.1 to 19.8% (p < 0.001). Conclusions Micronutrient deficiencies are prevalent in patients with obesity. Preoperative specialized multivitamin supplementation effectively reduces key deficiencies, particularly in iron, folic acid, and vitamin D. Future research should address residual deficiencies and evaluate long-term outcomes of prolonged supplementation.