This study aimed to investigate the association between oral disease burden and oral health related quality of life (OHRQoL) among overweight/obese (OW/OB) and normal weight (NW) Malaysian adolescents. A total of 397 adolescents were involved in the two-year prospective observational cohort study. OHRQOL was measured through a self-administered questionnaire containing the short version of the Malaysian Oral Health Impact Profile (OHIP[M]). Body mass index (BMI) was used for anthropometric measurement. Whilst, decayed, missing, and filled teeth (DMFT) index, Significant Caries Index (SiC), simplified basic periodontal examination (S-BPE), and gingival bleeding index (GBI) were used for clinical assessment tools. Higher dental caries prevalence was observed in the NW group while higher SiC was reported in the OW/OB group. Regardless of the obesity status, the prevalence of gingivitis (BPE code 1 and 2) was high in this study. A reduction of GBI prevalence was observed in the two-year follow-up results with an increased prevalence of OHRQoL impact in the OW/OB group compared to the NW group (p > 0.05). The findings from this study suggested that obesity status did not have influence over the burden of oral diseases and OHRQoL. It offers insights referring to the changes in adolescents’ oral diseases burden and OHRQoL.