Fungal secondary metabolites are bioactive compounds produced by fungi as by-products of metabolic processes. These metabolites include various chemical classes such as polyketides, terpenoids, alkaloids, and organic acids. However, they are not essential for the growth or reproduction of fungi, but play a crucial role in defence mechanisms, communication, and adaptation to environmental stresses. Many of these metabolites exhibit significant biological activities, making them valuable for various industrial and medical applications, including food preservation. This chapter describes the classification of fungal secondary metabolites and their biosynthesis, explaining the synthesis, regulation, and utilisation processes. It also explores the mechanism of action through which these metabolites inhibit microbial growth, thus maintaining the food quality and extending its shelf life. The current work primarily focuses on the applications of fungal secondary metabolites in food preservation as they offer various physiochemical properties and functional attributes. Industries, i.e. food packaging, coating, and fermentation, also highlight the capabilities of these metabolites to enhance the food preservation process. Despite their advantages, fungal metabolites face significant challenges for widespread use, including hefty production costs, stability concerns, and regulatory compliance. Addressing these obstacles could open new avenues by replacing harmful chemicals in the food industry with these natural compounds.