To evaluate the effectiveness of structured exercise appropriate the circadian rhythm in terms of blood sample test (BST), functionality and quality of life (QoL) in individuals with type 2 diabetes.This was a parallel-group, single-blind, crossover study. Thirty individuals with type 2 diabetes aged 35-65 years were enrolled in the study and allocated into 2 groups as the Morning Chronotype (MC) Group (n = 15) and the Evening Chronotype (EC) Group (n = 15) using Morningness-Eveningness Questionnaire which was used to determine the chronotypes. Participants were evaluated in terms of BST, functionality and QoL at the beginning of the study (T0), at 6 (T1), 12 (T2), and 18 (T3) weeks after the study started. A structured exercise program for 3 days a week over 6 weeks was applied in accordance with the chronotypes (T1-T2) and cross-controlled for the chronotypes (T2-T3). Significant differences were found in favor of the exercise given at the appropriate time for the chronotype in all parameters in both groups within groups (T0-T1-T2-T3) (p < 0.05). In the time∗group interactions, exercise in accordance with the appropriate chronotype in both groups provided the highest statistical improvement in all parameters (p < 0.05).It was concluded that structured exercise performed at the appropriate time for chronotype improves HbA1c, fasting blood glucose, HDL-LDL cholesterol, triglyceride, total cholesterol, functionality and quality of life in type 2 diabetes. This variation in blood values was observed to reflect the quantitative effects of exercise administered according to the circadian rhythm in individuals with type 2 diabetes.ClinicalTrials.gov (NCT04427488). The protocol of the study was registered at ClinicalTrials.gov (NCT04427488).