The term metabolite applies to a small molecule which is either an intermediate or product of metabolism.
Primary metabolites are organic compounds that are directly involved in the development process of an organism.
They are found in all animals and plants cells.
They play roles in the physiological processes.
For example, amino acids, sugars etc. are primary examples
Secondary metabolites basically occur in fungal, plant and microbial cells.
They are not directly involved in metabolic activities and perform assistive functions.
For example, alkaloids prevent the parasitic attack, flavonoids attract pollinators, involved in UV filtration, symbiotic nitrogen fixation and floral pigmentation.
Other examples include oils, rubber, gums, latex etc.