Endodontic disease with formation of periapical lesions (PALs) is one of the most common causes of chronic odontogenic sinusitis (ODS). It requires close collaboration between otolaryngologists and dentists, but the best sequence of management is still unknown. The aim of the present study is to clarify how radiological characteristics of teeth with PALs and previous root-canal treatment (RCT) influence the clinical evolution of the disease and to define the predictive value of its radiological and endoscopic features in determining the need for further surgical intervention. A total of 68 symptomatic patients with ODS with PALs were included in the study. The evaluation was performed by an otolaryngologist and a dentist based on a medical interview, nasal endoscopy, cold pulp testing and tomography images. Patients were prospectively followed for at least 12 months, during which nasal steroids, saline irrigations and RCT were administered. The criteria of disease improvement were: decrease of symptoms, healed sinonasal mucosa in endoscopy and radiological resolution of periapical radiolucency and sinus inflammation. Results showed that 9 (13%) patients improved after conservative treatment and 59 (87%) required further surgical intervention. Patients who improved after medical treatment and RCT were younger (p = 0.043) and had a greater distance from the top of the periapical lesion to the maxillary sinus' floor (p = 0.003). When expansion of PALs and bone destruction toward the maxillary sinus was observed on radiological imaging (p = 0.041), and when more than one tooth root was affected (p = 0.004), patients were more likely to require surgical intervention. In conclusion, the more roots that are affected and the closer the top of the PAL is to the maxillary sinus' floor, the greater the possibility of medical treatment and RCT failure. When the bone destruction extends into the maxillary sinus, patients eventually require both tooth extraction and FESS in order to resolve ODS completely.