Background: Malnutrition is a factor associated with mortality, particularly for older residents in long-term care facilities. Aim: This study aimed to evaluate the Minimum Data Set-based Screening for Nutritional Problem (MDS-SNP) and Mini Nutritional Assessment (MNA) in screening malnutrition among institutionalised older adults in Taiwan. Methods: A cross-sectional research design was employed and data from 131 residents were collected in northern Taiwan. Demographic and clinical variables such as cognitive function, activities of daily living, depression status, MDS-SNP, MNA, and dietary habits were obtained from residents’ profiles. Findings: The prevalence of malnutrition and risk of malnutrition defined by MNA were 32.8% (n = 43) and 30.5% (n = 40), respectively and 59.5% (n = 78) was at risk of malnutrition according to MDS-SNP. Multivariate logistic regression disclosed that some of the MDS-SNP items such as BMI and complaints of hunger, were significantly associated with MNA-defined risk and malnutrition but none of these were considered as trigger items in MDS-SNP. Discussion: Our study suggested that the MDS-SNP may be considered as an appropriate malnutrition screening tool. Screening nutritional status of older people is important because of its significant association with chronic conditions and function as well as quality of life. Conclusion: A modified MDS-based malnutrition screening tool in long-term care settings which considered BMI, complaints of hunger and nutritional approaches to deliver food as predictors is warranted.