Malnutrition is common, especially among older, hospitalised patients, and is associated with higher mortality, longer hospitalisation stays, infections, and loss of muscle mass. It is therefore of utmost importance to employ a proper method for dietary assessment that can be used for the identification and management of malnourished hospitalised patients. In this study, we propose an automated Artificial Intelligence (AI)-based system that receives input images of the meals before and after their consumption and is able to estimate the patient’s energy, carbohydrate, protein, fat, and fatty acids intake. The system jointly segments the images into the different food components and plate types, estimates the volume of each component before and after consumption, and calculates the energy and macronutrient intake for every meal, based on the kitchen’s menu database. Data acquired from an acute geriatric hospital as well as from our previous study were used for the fine-tuning and evaluation of the system. The results from both our system and the hospital’s standard procedure were compared to the estimations of experts. Agreement was better with the system, suggesting that it has the potential to replace standard clinical procedures with a positive impact on time spent directly with the patients.