Aflatoxins are a naturally occurring group of toxins produced by two species of the ubiquitous fungus Aspergillus (A. flavus and parasiticus) when they grow under favourable conditions for toxin formation. They may be contained in everyday food and feed, and they can cause damage to the health of humans and animals. All over the world, national authorized bodies have established regulations to limit the levels of aflatoxins in food and feed. The aim of this study was to determine aflatoxin B1 contamination in different types of chilli, peanut, and related products from the local area. The detection instruments used in this work was HPLC. A total of 350 samples collected from January, 2021 to March, 2022 for various types of chilli, peanut and related products were analyzed in the Laboratory of Small Scale Industries Department. According to FDA guideline of 20 ppb, about 20% of the tested samples were over the guideline value. In this paper, the challenges that we are facing while detection of aflatoxin B1 in various types of chilli, peanut, and related products, including sample preparation, methods, equipment, consumables, manpower, and facilities, will be discussed.