In the last sixty years, there has been an alarming decline in food quality and a decrease in a wide variety of nutritionally essential minerals and nutraceutical compounds in imperative fruits, vegetables, and food crops. The potential causes behind the decline in the nutritional quality of foods have been identified worldwide as chaotic mineral nutrient application, the preference for less nutritious cultivars/crops, the use of high-yielding varieties, and agronomic issues associated with a shift from natural farming to chemical farming. Likewise, the rise in atmospheric or synthetically elevated carbon dioxide could contribute to the extensive reductions in the nutritional quality of fruits, vegetables, and food crops. Since ancient times, nutrient-intense crops such as millets, conventional fruits, and vegetables have been broadly grown and are the most important staple food, but the area dedicated to these crops has been declining steadily over the past few decades and hastily after the green revolution era due to their poorer economic competitiveness with major commodities such as high-yielding varieties of potato, tomato, maize, wheat, and rice. The majority of the population in underdeveloped and developing countries have lower immune systems, are severely malnourished, and have multiple nutrient deficiency disorders due to poor dietary intake and less nutritious foods because of ignorance about the importance of our traditional nutrient-rich diets and ecofriendly organic farming methods. This critical review emphasizes the importance of balance and adequate nutrition as well as the need to improve soil biodiversity and fertility: those are main causes behind the decline in nutritional density. There is also emphasis on a possible way out of alleviating the decline nutritional density of food crops for the health and well-being of future generations.