Impaired tissue oxygenation is the key pathomechanism in the development of organ dysfunction in shock; mitochondrial impairment can aggravate the condition. However, measuring tissue oxygenation directly and non-invasively still poses a clinical challenge. A novel device (COMET) allows the assessment of mitochondrial oxygen metabolism using the Protoporphyrin IX Triplet State Lifetime Technique (PpIX-TSLT). Critically ill patients, especially in sepsis, often exhibit oedema which may interfere with the COMET measurement. Furthermore, patients' physical activity level differs significantly before and during hospitalisation. Thus, the aim of this study was to identify the effects of physical activity and body composition on mitochondrial oxygen tension (mitoPO2) and consumption (mitoVO2) in healthy controls (N = 40). Furthermore, the study tested the repeatability of the COMET variables and identified covariates. Multiple COMET measurements were performed before (T1, T2), during and after (T3, T4) ergometry. Body composition was assessed by bioimpedance analysis. Physiological variables (blood pressure, heart rate, oxygen saturation) were recorded. In the analytical sample (n = 26), physical activity significantly decreased mitoVO2; other COMET variables remained unchanged between T2 and T3. During ergometry, mitoPO2 increased significantly. The distribution of body water significantly influenced mitoVO2. In our setting, the method demonstrated moderate repeatability. Variables of fitness (heart rate recovery, phase angle and physical activity level), signal quality and duration of exposure to 5-aminolevulinic acid (obligatory for PpIX-TSLT) were identified as significant covariates of mitoVO2. Mitochondrial oxygen delivery (mitoDO2) was established as a new variable of COMET analysis. Results of this pilot study should be validated in future studies.