Plant-based diets (PBD) that consist of whole grains, fruits, berries, vegetables, nuts, seeds, and legumes have been shown to yield positive health outcomes. In addition to the beneficial impact, PBD can be more sustainable for the planet. The production of animal-based proteins is the main source of greenhouse gas emissions in agriculture, and the consumption of highly processed meat has been associated with negative health outcomes. Therefore, plant-based protein rich (PBPR) options are needed. Plant-based foods are often processed in various ways to improve their nutritional content and sensory properties. Processing techniques like cutting and peeling can be gentler on the raw material, while extraction of components can be more intense. During processing some biochemical changes can often occur, such as changes in the structures and amounts of existing compounds and formation of new compounds. In addition, unwanted compounds can be removed and beneficial compounds lost from the raw material. The aim of this thesis was to examine the composition of small molecules in plant-based protein-rich foods and the impact of various food technological processing techniques on them. A metabolomics approach using liquid chromatography with mass spectrometry (LC–MS) was used with reversedphase (RP) and hydrophilic interaction chromatography (HILIC) to cover a wide range of metabolites. The first study focused on commercially available PBPR foods where products made from different raw materials with varying processing techniques were analysed. In addition, existing food processing classification systems were used to assess whether they agree with the study findings regarding PBPR foods. In the second study, four different fermentation techniques were used to produce lupin-based beverages and changes in their biochemical compositions were analysed with the same metabolomics approach. The findings from both of these studies show that food processing can have major effects on the biochemical compounds present in plant-based foods. Fermentation stood out as a promising technique to possibly improve the bioavailability of beneficial compounds in soy-based foods in the first study, whereas these same compounds were almost absent in products made with purified protein concentrates or isolates. When the existing food processing classifications were used with these products, most of the foods were categorised as so-called ultra-processed foods, and some conflicting results were observed. In lupin-based beverages, the different fermentation techniques increased the abundances of lactic acid derivatives and decreased the abundances of vitamin B compounds. By selecting the most suitable fermentation technique depending on the desired results, lupins could be used to produce protein-rich alternatives to animal-based milk in the future. The amount of plant-based foods in the diet, especially legumes, vegetables and fruits, should be increased for both environmental and health reasons. While the consumption of plant-based foods is generally beneficial, the impact of foods consisting of refined plant-based materials on human health is not fully understood yet. Plant-based foods often require processing and its impact on the comprehensive biochemical composition of these foods needs to be studied in greater detail. When assessing the healthiness of PBPR foods it would be important to consider the content and profile of nutrients and other potentially health-beneficial biochemicals over their possible classification categories, as plant-based foods with beneficial compounds can often be classified as “ultraprocessed”. This thesis provides valuable insight into these aspects, and in particular demonstrates the possibilities of food fermentation to develop PBPR foods.