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Recent findings show that beneficial microbes are essential for establishing and maintaining a healthy microbiome in the soil, plants and humans alike. Many of the beneficial microbes in the human gut can be obtained from eating healthy food, but most current healthy food concepts still lack the aspect of healthy microbes. It is hardly known that many of these beneficial microbes in healthy food are also essential for protecting plants from bacterial, fungal and viral diseases and that the large use of pesticides and herbicides in agriculture challenges the life of gut, plant and soil microbes - and that it is the soil microbiome which is the ultimate source of microbial partners for plants, animals and humans alike. Research has shown that soil and plants from intensive agriculture lacks essential microbiota to produce healthy food and feed. Using high throughput sequencing of soil and microbial samples and artificial intelligence, we developed a strategy for the identification and potential rehabilitation of impoverished soils and plants. Our results show that microbial input from biobanks derived from healthy soils and plants can improve soil and plant microbiome composition and productivity. We propose a novel concept for transforming agriculture to produce healthy food on a global scale. We believe that healthy food forms the basis of human health and that we must aim to make healthy food available to every human on this planet.