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Abstract Background Metabolic syndrome (MetS) in older adults with hypertension, diabetes, and hyperlipidemia increases the risks of cardiovascular diseases by 2.5 times and type 2 diabetes by five times. This study aimed to explain the multilevel relationships between health service system factors and individual-level factors influencing the control of MetS among older adults with NCDs receiving health care services at the NCD Plus clinics of hospitals in 1 year. Methods This cross-sectional analytical study employed a systematic sampling method to have two groups of samples from 4 regions of Thailand: (1) 600 older adults having at least one diagnosis of NCDs receiving services at NCD Plus clinics and (2) 12 nurses in charge of the NCD Plus clinics at the hospitals providing services to these patient samples. Data were analyzed using multilevel logistic regression analysis. Results 24% of older adults with NCDs can control MetS within one year. The MetS escalation from the initial assessment to 1-year follow-up varied according to the level of the hospitals. The transition from MetS to non-MetS status was rare in older adults with NCDs. Among health service system factors, complete screening for MetS influenced 1-year MetS control (95% CI [1.06, 2.92]). Older adults who were female and who had polypharmacy had a 66% (95% CI [0.22, 0.53]) and a 54% (95% CI [0.29 − 0.71]) reduction chance in MetS control. Older adults, who were ≥ 80 years old, labor-employed, healthy dietary patterns, and medication adherence increased chances of controlling MetS by 2.38 times (95% CI [1.12, 5.05]), 2.14 times (95% CI [1.03, 4.42]), 1.61 times (95% CI [1.06–2.46]), and 3.18 times (95% CI [1.51, 6.70]), respectively. Conclusions NCDs Plus clinics that provide complete screening for MetS significantly enhance their effectiveness in reducing the proportion of older adults with MetS. In addition, the service should pay attention to older adults who are female, are retired, and take multiple medications to achieve MetS control better. The insights gained from such an analysis could be instrumental in pinpointing the resources necessary to bolster the efficacy of NCD Plus clinics.