Background Current near-infrared spectroscopy (MRS)-based systems for continuous flap monitoring are limited to flaps which carry a cutaneous paddle. As such, this useful and reliable technology has not previously been applicable to muscle-only free flaps where other modalities with substantial limitations continue to be utilized. Methods We present the first MRS probe which allows continuous monitoring of local tissue oxygen saturation (StO(2)) directly within the substance of muscle tissue. This probe is flexible, subcentimeter in scale, waterproof, biocompatible, and is fitted with resorbable barbs which facilitate temporary autostabilization followed by easy atraumatic removal. This novel device was compared with a ViOptix T.Ox monitor in a porcine rectus abdominus myocutaneous flap model of arterial and venous occlusions. During these experiments, the T.Ox device was affixed to the skin paddle, while the novel probe was within the muscle component of the same flap. Results The intramuscular MRS device and skin-mounted ViOptix T.Ox devices produced very similar StO(2) tracings throughout the vascular clamping events, with obvious and parallel changes occurring upon vascular clamping and release. The normalized cross-correlation at zero lag describing correspondence between the novel intramuscular MRS and T.Ox devices was >0.99. Conclusion This novel intramuscular MRS probe offers continuous monitoring of oxygen saturation within muscle flaps. This experiment demonstrates the potential suitability of this intramuscular MRS probe for the task of muscle-only free flap monitoring, where MRS has not previously been applicable. Testing in the clinical environment is necessary to assess durability and reliability.