Food is a complex soft matter, because various components, such as proteins, lipids, and carbohydrates, are self-assembled via non-covalent, colloidal interactions and form hierarchical structures at multiple length scales. Soft matter scientists have shown an increasing interest in understanding the general principles governing the food structure formation. During the last several decades, an increasing number of studies have shown that the maintenance of healthy gastrointestinal tract and its microbiome is essential for human health and wellbeing. The realization of the importance of the gastrointestinal microbiome has led to the development of probiotics, which are defined as living bacteria that confer a health benefit on the host. Probiotic bacteria and enzymes can be delivered to the intestinal system by formulating appropriate carriers and including these into food ingested by humans. Despite this simple statement, it involves many challenges in the field of soft matter science. This review aims to highlight how the key concepts in soft matter science can be used to design, characterize, and evaluate self-assembled formulations of probiotics and enzymes based on lipids and biopolymers. The topics covered in this review includes the emulsification of oil-water mixtures, the self-assembly of lipids and polymers at interfaces, the electrostatics and viscoelasticity of interfaces, and the wetting/adhesion of colloidal particles.