Malnutrition and sarcopenia often coexist in rehabilitation patients, although they are often overlooked and undertreated in clinical practice. This cross-sectional study aimed to clarify the prevalence of the coexistence of malnutrition and sarcopenia (Co-MS) and its associated factors in convalescent rehabilitation wards in Japan. Consecutive patients aged ≥ 65 years in convalescent rehabilitation wards between November 2018 and October 2020 were included. Malnutrition and sarcopenia were determined by the Global Leadership Initiative on Malnutrition (GLIM) criteria and the Asian Working Group for Sarcopenia (AWGS 2019) criteria, respectively. Patients who presented both with malnutrition and sarcopenia were classified as Co-MS. Potentially associated factors included age, sex, days from onset to admission of rehabilitation wards, reason for admission, pre-morbid functional dependency, comorbidity, activities of daily living, swallowing ability, and oral function and hygiene. The prevalence of malnutrition, sarcopenia, and Co-MS was calculated. Binary logistic regression analyses were performed to compute odds ratios (ORs) and the 95% confidence interval (CI) of possible associated factors for each condition. Overall, 601 patients were eligible for the analysis (median 80 years old, 355 female patients, 70% cerebrovascular disease). Co-MS, malnutrition, and sarcopenia were found in 23.5%, 29.0%, and 62.4% of the enrolled patients, respectively. After adjustment, onset–admission interval (OR = 1.04; 95%CI = 1.02 to 1.06), hospital-associated deconditioning (OR = 4.62; 95%CI = 1.13 to 18.8), and swallowing ability (Food Intake LEVEL Scale) (OR = 0.83; 95%CI = 0.73 to 0.93) were identified as independent explanatory factors of Co-MS. In conclusion, Co-MS was prevalent in geriatric rehabilitation patients; thus, healthcare professionals should be aware of the associated factors to detect the geriatric rehabilitation patients who are at risk of both malnutrition and sarcopenia, and to provide appropriate treatments.