Background The confusion between a phlebolith and a sialolith in the floor of the mouth can pose serious surgical risks, making it essential to define appropriate complementary imaging studies. Case presentation We present the case of a patient with right submandibular sialolithiasis suspected by computed tomography. A previous attempt at extraction in another centre, under local anesthesia, was interrupted due to profuse bleeding, preventing the localization and removal of the calculi. Due to our pre-surgical study protocol using magnetic resonance sialography (MR-Si), a low-flow vascular malformation with internal phleboliths was revealed, without involvement of the salivary duct. As a result, the planned sialendoscopy was cancelled, and a follow-up approach was chosen given the asymptomatic nature of the condition. Conclusions This case underscores the importance of standardizing radiological studies for salivary gland and floor of-mouth pathology, highlighting MR-Si for its high sensitivity and specificity. Therefore, MR-Si enables more precise surgical planning and helps prevent unnecessary intraoperative complications