Over the last few years, portable Near-Infrared Spectroscopy (NIRS) technology has been suggested for determining metabolic/ventilator thresholds. This systematic review and meta-analysis aimed to assess the reliability of a portable muscle oxygenation monitor for determining thresholds during exercise testing. The proposed PICO question was: Is the exercise intensity of muscle oxygenation thresholds, using portable NIRS, reliable compared with lactate and ventilatory thresholds for exercise intensity determined in athletes? A search of Pubmed, Scopus and Web of Science was undertaken and the review was conducted following PRISMA guidelines. Fifteen articles were included. The domains which presented the highest biases were confounders (93% with moderate or high risk) and participant selection (100% with moderate or high risk). The intra-class correlation coefficient between exercise intensity of the first ventilatory or lactate threshold and the first muscle oxygenation threshold was 0.53 (obtained with data from only 3 studies), whereas the second threshold was 0.80. The present work shows that although a portable muscle oxygenation monitor has moderate to good reliability for determining the second ventilatory and lactate thresholds, further research is necessary to investigate the mathematical methods of detection, the capacity to detect the first threshold, the detection in multiple regions, and the effect of sex, performance level and adipose tissue in determining thresholds.