Currently, herbs, medicinal spices, green medicine, or traditional Chinese medicine has gained many followers in the world, especially as a way of life and as an alternative to the indiscriminate use of synthetic medicines such as antibiotics. These natural products are rich in secondary metabolites or phytochemicals, which are chemical compounds of relatively complex structures and restricted distribution; these compounds have defensive functions against insects, bacteria, fungi, parasites, and viruses. Likewise, several studies have shown their effectiveness in the prevention and treatment of several diseases such as cancer, autoimmune diseases, gastrointestinal diseases, diabetes, neurodegenerative diseases, Crohn's disease, and human immunodeficiency virus (HIV), among others. In addition, this review addresses the mechanisms of action of the herbs and medicinal spices on intestinal microbiota, increasing competitive exclusion in the intestinal membrane and inhibiting bacterial translocation and damage to the intestinal barrier.