The increased usage of alternative Ayurvedic treatments as potential health-beneficial therapies emphasizes the importance of studying its efficacy in sound placebo-controlled intervention trials. An example of such a traditional Ayurvedic herbal preparation is Mohana Choorna, a mixture composed of 20 different herbs and used to prevent and treat type 2-diabetes (T2D). We studied the efficacy of “Mohana Choorna” on T2D-related parameters in subjects with impaired glucose tolerance. In a double blind, placebo-controlled cross-over trial, 19 overweight (BMI > 27 kg/m2) subjects aged 50–70 years with an impaired glucose tolerance received two four-week interventions, i.e., herbal or placebo with a four-week wash-out between interventions. HbA1c, glucose, insulin, triglycerides, cholesterol, blood pressure and augmentation index were measured before and after both interventions at fasting and during a glucose tolerance test. After both interventions, urine was collected to measure treatment exposure using LCMS-based metabolomics and whole genome gene-expression in adipose tissue of 13 subjects. The herbal intervention did not affect plasma glucose triglycerides, cholesterol, blood pressure or the augmentation index but showed a trend towards an increased insulin, HOMA-IR and postprandial insulin levels (p = 0.054, p = 0.056 and p = 0.095 respectively). An increase in expression of inflammation-related gene sets in adipose tissue was observed after the herbal intervention compared to placebo. Urine metabolomic analysis did not reveal a correlation of the presence of specific plant metabolites with “health markers”. Our findings suggest that there is no substantiating evidence to claim that four weeks’ use of the Ayurvedic herbal supplement Mohana Choorna beneficially affects glucose homeostasis.