MicroRNAs (miRNAs) are small non-coding RNAs, and adipose tissue is a major source of circulating miRNAs that may regulate body fat distribution. We investigated whether changes in circulating adipose-derived miRNAs (miR-99a-5p, miR-99b-5p, and miR-100-5p) were related to improvements in visceral and ectopic fat depots in abdominal obese adults who participated in the CENTRAL diet-and-lifestyle intervention trial. We further tested whether changes in these miRNAs were related to improved glucose metabolism and insulin sensitivity after the intervention. Plasma levels of miRNAs were measured both at baseline (n=227) and 18 months (n=157) after the intervention; changes in miRNAs from baseline to 18 months were calculated. Magnetic resonance imaging (MRI) was performed to assess visceral adipose tissue (VAT), intrahepatic fat %, and pancreatic fat %. At baseline, higher levels of miR-99a-5p and miR-100-5p were associated with greater intrahepatic fat (p <0.0001 for both). The study participants showed considerable differences in circulating miRNA changes in response to the diet/physical activity intervention, and greater decreases in miR-99a-5p were associated with greater improvements in VAT (p=0.0027) and intrahepatic fat (p=0.015) at 18 months. Similarly, the reduction of miR-100-5p was related to 18-month improvements in VAT (p=0.0025) and intrahepatic fat (p=0.0023). Further, decreases in miR-99b-5p (p=0.038) and miR-100-5p (p=0.033) levels were associated with improved pancreatic fat at 18 months. Participants with more decreases in miR-99b-5p had reduced pancreatic fat and were also characterized as having lower glucose levels and higher HOMA of β-cell function at the end of the intervention. Our findings underscore the importance of changes in specific adipose-derived circulating miRNAs in improving diabetogenic fat depots and insulin sensitivity during the intervention for abdominal obese patients.