Background: Allergic fungal sinusitis (AFS) has been increasingly recognized over recent decades. This study aimed to evaluate the definitive outcomes of endoscopic sinus surgery (ESS) with and without partial middle turbinate resection (PMTR). Methods: A prospective, cross-sectional study was conducted on 40 patients diagnosed with AFS. They were randomized equally into two groups. Group A underwent ESS with preservation of the middle turbinate, while Group B received ESS with additional PMTR. Results: Preoperative Lund-Kennedy and SNOT-22 scores were comparable between groups. At 4 weeks postoperatively, no significant difference in Lund-Kennedy scores was observed. However, Group B showed significantly lower Lund-Kennedy scores at 3 and 6 months (P = 0.040 and < 0.001, respectively). Additionally, Group B had significantly lower SNOT-22 scores at 6 months (P < 0.001). Minor bleeding occurred in one patient (5%) from Group A and two (10%) from Group B, with no significant difference. There were no reports of cerebrospinal fluid rhinorrhea, orbital injury, or olfactory dysfunction in either group. Recurrence was significantly higher in Group A (30%) compared to Group B (5%) (P = 0.037). Conclusion: Adding partial middle turbinate resection to standard endoscopic sinus surgery in patients with allergic fungal sinusitis is associated with improved long-term clinical outcomes, including better symptom control, reduced endoscopic findings of inflammation, and lower recurrence rates, without increasing the risk of significant complications.