This study examined the effect of dietary consumption of carbohydrates (CHO) on the blood lactate to rating of perceived exertion (La:RPE) ratio during an intense micro-cycle of exercise training. This ratio is a proposed biomarker of exercise training stress and potential indicator for under- or overtraining in athletes. Sixteen male athletes were randomly assigned into two groups; high CHO (H-CHO; 60% of daily caloric intake) and low CHO (L-CHO; 30% of daily caloric intake). Diets were controlled the day before and for the three days of the micro-cycle. The micro-cycle consisted of three successive days of 60 minutes of intense cycling (∼70% of VO2peak). Blood samples were obtained immediately before and after exercise (post) on each day of exercise training (D1, D2, D3) and were analyzed for blood lactate. Rating of perceived exertion (RPE) scores were taken at the end of each exercise session and combined with the post exercise lactate value to form the La:RPE ratio. An analysis of variance (ANOVA) showed a significant difference between the La:RPE ratio for the H-CHO and L-CHO groups at D3 even though the exercise intensity was not significantly different between the groups. Specifically, the ratio was significantly (p < 0.02) lower on D3 in the L-CHO group (∼31% lower) than in the H-CHO group. From these findings it is recommended that diet needs to be monitored when using the La:RPE ratio as an exercise training biomarker to determine whether an athlete is truly under-training or overtraining. Athletes or coaches that use the La:RPE ratio as a training biomarker, but do not monitor dietary CHO intake need to interpreted their findings carefully.