Objectives The objectives of this study were 1) to investigate the prevalence and co-existence of frailty and malnutrition and 2) to identify factors related to frailty (including malnutrition) according to the level of frailty. Methods Data collection was conducted from July 11, 2021, to January 23, 2022, in 558 older adults residing in 16 long-term care facilities (LTCFs) in Korea. The FRAIL-NH and Mini-Nutritional Assessment short form were used to measure frailty and nutrition, respectively. The data analysis included descriptive statistics and a multivariate logistic regression. Results The mean age of the participants was 83.68 (± 7.39) years. Among 558 participants, 37 (6.6%), 274 (49.1%), and 247 (44.3%) were robust, prefrail, and frail, respectively. At the same time, 75.8% were categorized as having malnutrition status (malnourished: 18.1%; risk of malnutrition: 57.7%), and 40.9% had co-existing malnutrition and frailty. In the multivariate analysis, malnutrition was identified as the major frailty-related factor. Compared with a normal nutritional status, the incidence of frailty in the malnutrition group was 10.35 times (95% CI: 3.78–28.36) higher than the incidence of robustness and 4.80 times (95% CI: 2.69–8.59) higher than the incidence of prefrail. Conclusion The prevalence of frailty and malnutrition, and their co-existence, among older adults residing in LTCFs was high. Malnutrition is a major factor that increases the incidence of frailty. Therefore, active interventions are needed to improve the nutritional status of this population.