BackgroundLong intervals between patient visits and limited time with patients can result in clinical inertia and suboptimal achievement of treatment goals. These obstacles can be improved with a multidisciplinary care program. The present study aimed to assess the impact of such a program on glycemic control and cardiovascular risk factors.MethodsIn a randomized, parallel-group trial, we assigned 263 patients with poorly controlled type 2 diabetes mellitus (T2DM) to either a control group, standard care program, or a multidisciplinary care program involving a senior family physician, clinical pharmacy specialist, dietician, diabetic educator, health educator, and social worker. The participants were followed for a median of 10 months, between September 2013 and September 2014. Glycated hemoglobin (HbA1c), fasting blood glucose (FBG), lipid profiles, and blood pressure (BP) were measured. The assignment was blinded for the assessors of the study outcomes. The study registry number is.ResultsIn the intervention group, there were statistically significant (p < 0.05) post-intervention (relative) reductions in the levels of HbA1c (−27.1%, 95% CI = −28.9%, −25.3%), FBG (−17.10%, 95% CI = −23.3%, −10.9%), total cholesterol (−9.93%, 95% CI = −12.7%, −7.9%), LDL cholesterol (−11.4%, 95% CI = −19.4%, −3.5%), systolic BP (−1.5%, 95% CI = −2.9%, −0.03%), and diastolic BP (−3.4%, 95% CI = −5.2%, −1.7%). There was a significant decrease in the number of patients with a HbA1c ≥10 (86 mmol/mol) from 167 patients at enrollment to 11 patients after intervention (p < 0.001). However, the intervention group experienced a statistically significant increase in body weight (3.7%, 95% CI = 2.9%, 4.5%). In the control group, no statistically significant changes were noticed in different outcomes with the exception of total cholesterol (−4.10%, p = 0.07). In the linear regression model, the intervention and the total number of clinic visits predicted HbA1c improvement.ConclusionsImplementation of a patient-specific integrated care program involving a multidisciplinary team approach, frequent clinic visits, and intensified insulin treatment was associated with marked improvement in glycemic control and cardiovascular risk factors of poorly controlled T2DM patients in a safe and reproducible manner.Trial registrationISRCTN Identifier: ISRCTN83437562 September 19, 2016 Retrospectively registered.Electronic supplementary materialThe online version of this article (10.1186/s12875-017-0677-2) contains supplementary material, which is available to authorized users.