Introduction: Benign nodular goiter may be associated with swallowing difficulties, but insight into the associated pathophysiology is limited. The aim of this study was to investigate the effect of surgery on the degree of esophageal compression, and its correlation to swallowing difficulties. Methods: Esophageal compression and deviation were evaluated blindly on magnetic resonance imaging (MRI) of the neck, prior to and 6 months after thyroid surgery for symptomatic benign goiter. Goiter symptoms and swallowing difficulties were measured by the Goiter Symptom Scale of the Thyroid-Specific Patient-Reported Outcome (ThyPRO) questionnaire. Cohen’s d was used for evaluating effect sizes (ES). Results: Sixty-four patients completed the study. Before surgery, median goiter volume was 57 (range 14–642) mL. The smallest cross-sectional area of the esophagus (SCAE) increased from a median of 95 (47–147) to 137 (72–286) mm² (ES = 1.31, p < 0.001). Median esophagus width increased from 15 (range 10–21) to 17 (range 12–24) mm (ES = 0.94, p < 0.001) after surgery, while no statistically significant change was observed for the sagittal dimension (anterior-to-posterior), thus reflecting an increasingly ellipsoid esophageal shape. Median esophageal deviation decreased moderately after surgery from 4 (0–23) to 3 (0–10) mm (ES = 0.54, p = 0.005). The goiter symptom score improved considerably from (mean ± SD) 40 ± 21 to 10 ± 10 points (ES = 1.5, p < 0.001) after surgery, and the improvements were associated with improvements in SCAE (p = 0.03). Conclusions: In patients with goiter, thyroidectomy leads to substantial improvements in esophageal anatomy, as assessed by MRI, and this correlates with improved swallowing symptoms. This information is valuable in qualifying the dialogue with goiter patients, before deciding on the mode of therapy. Clinicaltrials.gov (NCT03072654).