Leading a healthy lifestyle has become one of the most challenging goals in today's society due to our sedentary lifestyle and poor eating habits. As a result, national and international organisms have made numerous efforts to promote healthier food diets and physical activity habits. However, these recommendations are sometimes difficult to follow in our daily life and they are also based on a general population. As a consequence, a new area of research, personalised nutrition, has been conceived focusing on individual solutions through smart devices and Artificial Intelligence (AI) methods. This study presents the AI4Food-NutritionDB database, the first nutrition database that considers food images and a nutrition taxonomy based on recommendations by national and international organisms. In addition, four different categorisation levels are considered following nutrition experts: 6 nutritional levels, 19 main categories (e.g., "Meat"), 73 subcategories (e.g., "White Meat"), and 893 final food products (e.g., "Chicken"). The AI4Food-NutritionDB opens the doors to new food computing approaches in terms of food intake frequency, quality, and categorisation. Also, in addition to the database, we propose a standard experimental protocol and benchmark including three tasks based on the nutrition taxonomy (i.e., category, subcategory, and final product) to be used for the research community. Finally, we also release our Deep Learning models trained with the AI4Food-NutritionDB, which can be used as pre-trained models, achieving accurate recognition results with challenging food image databases.