A prospective study was conducted to investigate the impact of treatment burden and health literacy on medication adherence among older adults with multiple chronic conditions (MCC) and to explore the potential moderating effects of demographic and clinical factors. Face-to-face structured interviews were conducted among older adults aged 60 and above using the Burden of Treatment Questionnaire (TBQ-15), Short Form Health Literacy Questionnaire (HLS-SF12), and Malaysia Medication Adherence Assessment Tool (MyMAAT). This study included 346 older adults aged 60 years and above with two or more chronic conditions (n = 346). Hypertension (30.2%), hyperlipidemia (24.0%), and diabetes (18.0%) were the most reported chronic conditions among participants. The mean score of treatment burden was 53.4 (SD = 28.2), indicating an acceptable burden of treatment. The mean score of health literacy was 16.4 (SD = 12.6), indicating a limited health literacy level among participants; meanwhile, the mean score of medication adherence was 32.6 (SD = 12.3), indicating medication non-adherence among participants. Medication adherence was significantly correlated with treatment burden (r = -0.22, p < 0.0001), health literacy (r = 0.36, p < 0.0001), number of chronic conditions (r = -0.23, p < 0.0001), and age (r = -0.11, p < 0.05). The study findings emphasize that multimorbid older adults with high treatment burdens and low health literacy are more likely to have poor medication adherence. This underscores the importance for clinicians to address these factors in order to improve medication adherence among older adults with multiple chronic conditions (MCC).