Aim: This case report aims to describe the management of a maxillary lateral incisor with a palatogingival groove (PGG) associated with a complex lesion. Background: The PGG is a rare developmental anomaly that involves the lingual surface of the maxillary incisors and extends for varying distances and depths on the root surface. This anomaly is usually inconspicuous and funnel-shaped, which forms a niche where bacterial plaque and calculus can accumulate to levels significant for pathological changes resulting in endodontic and periodontal lesions. These grooves are easily overlooked as etiologic factors, as they are concealed by the periodontal tissues. Case description: This paper describes the successful management of a rare case of maxillary lateral incisor with an accessory root, two canals, and a complex or type III PGG with a endodontic–periodontic lesion using a multidisciplinary approach. Conclusion: Recognizing PGG as the initiator of pathology is critical for the successful treatment and favorable prognosis of the affected tooth. Clinical significance: This case report highlights the importance of three-dimensional (3D) imaging using cone beam computed tomography (CBCT) that can provide accurate and sensitive information to assess and plan the treatment of the teeth with PGG. It also emphasizes that with the development of newer materials and diagnostic tools, clinicians need a detailed understanding of the characteristics, treatment, and prognosis of PGG to successfully manage the condition.