A very unusual, interesting, and challenging case of a 24-year-old female who was born with three openings in the neck. The patient had chronic abdominal gaseous distention, recurrent abdominal pain, and constipation since early infancy. The patient presented in emergency with acute painful red, hot, and tender swelling in the left upper cervical area. Laboratory studies showed high inflammatory markers and a provisional diagnosis of abscess with a sinus was made. The patient underwent an emergency incision and drainage. Sinus recurred and a sinogram showed it to be a residual cyst in the left submandibular salivary gland. The total cyst excision was attempted with resultant recurrence and grade IV facial nerve palsy. Post-operatively recurrent infections caused by Methicillin-resistant Staphylococcus aureus (MRSA) required several courses of oral and intravenous broad-spectrum antibiotics with several hospital admissions with no resolution in sight. Subsequent ultrasound and magnetic resonance imaging showed a residual infected cyst, cutaneous sinus, and a fistula opening in the left ear canal. A diagnosis of branchial cyst type II of the first brachial cleft remnant with a fistula was established with bilateral branchial fistulas of the second branchial remnants and the associated colorectal hypoganglionosis based on radiological studies. The patient refused any further operative interventions. Therefore, the option of conservative treatment of hypoganglionosis with holobiotics consisting of prebiotics, probiotics and postbiotics, laxatives, dietary changes, lifestyle modifications, and dietary supplements started. All antibiotics were stopped. These therapies resulted in the resolution of residual first branchial remnants and recurrent MRSA infections with the improvement in the facial nerve palsy from grade V to grade III-IV together with an excellent cosmetic and functional result. The patient is doing well at follow-ups being infection-free for 18 months and repeat contrast-enhanced computed tomogram (CECT) has shown complete resolution of the residual cyst, sinus, and fistula with fibrosis.