Abstract Background Obesity in children is one of the most severe public health challenges of the current century and Type 2 Diabetes Mellitus (T2DM) frequency is also escalating. More so, the importance of process evaluation (PE) in complex interventions is increasingly recognized. The present review, aims to identify the effectiveness in terms of body composition parameters in a generation of articles to prevent obesity and T2DM in children. We hypothesise that those studies reporting PE applying the latest implementation guidelines suggested by the researchers would potentially show positive changes in body composition compared to those not reporting it. Additionally, we will evaluate the implementation degree of PE in those articles considering it and describe the PE subcomponents. Lastly, we aim to assess the intervention target used and its results. Methods A literature review was performed in parallel by 2 independent reviewers. A final number of 41 studies were selected for inclusion criteria. Results Meta-analysis of BMI and zBMI found non-significant effects of the proposed interventions. Sub-group analysis revealed only a significant effect in studies which performed PE. Moreover, PE was reported in 42% effective studies and 57% non-effective studies. Fidelity and satisfaction were the most implemented PE subcomponents, although there was a generally low grade of PE use (7/41). The highest proportion of effectiveness (83%) was shown in interventions of physical activity alone while the intervention most used was 3-arm target (diet, PA and BS). Conclusions Overall, obesity and T2DM prevention studies included in this review are not effective in terms of BMI and zBMI. Those studies performing PE reported to be effective in terms of BMI, while studies not reporting PE did not have positive results in terms of BMI and zBMI. In addition, none of the intervention studies included all PE indicators and most studies, which included PE in their interventions, did not provide full report of the PE components, according to the guidelines used for the present review. PROSPERO registration number: CRD42018093667.