The relationship between low physical function (LPF) at discharge and food intake percentage (FIP) during hospitalization is unclear. We aimed to clarify the relationship between LPF at discharge and FIP and the change in nutritional status during hospitalization in elderly patients with heart failure (HF), and determine cutoff values for FIP and change in nutritional status during hospitalization. We included 431 consecutive patients aged ≥ 65 years who were hospitalized for HF and underwent cardiac rehabilitation (CR) from 2017 to 2019. Physical function at discharge was classified into two groups according to the Short Performance Physical Battery (SPPB): low physical function (LPF) (SPPB ≤ 9) and high physical function (HPF) (SPPB > 9). We compared background, clinical parameters, pre-hospital walking level, CR progress, nutritional factors during hospitalization including FIP of the main dish and side dish, and changes in nutritional status using the Geriatric Nutritional Risk Index (ΔGNRI) at admission and discharge. Multiple logistic regression analysis was also performed. The final analysis included 213 patients (age, 81.6 years) divided into the LPF (n = 136) and HPF groups (n = 77). The LPF group showed low FIP and a high ΔGNRI value. Multivariate analysis showed FIP main dish, ΔGNRI, worsening renal function, pre-hospital walking level, and days to start of walking to be factors influencing LPF at discharge. Respective cutoff values for FIP main dish and ΔGNRI predicting LPF at discharge were 82.2% and 4.24. FIP main dish during hospitalization and ΔGNRI were associated with LPF at discharge.