The majority of pathologies in poultry are linked to intestinal chronic inflammation due to a disbalance of the gut microbiota. Thus, a healthy microbiota drives the gut integrity, and the gut’s biological and metabolic functionalities, including efficacious use of nutrition, but also immunity, and neuroendocrine systems. However, many external factors are disturbing a stable, healthy gut microbiota. Heat stress, dysbiosis, leaky gut syndrome, and mycotoxins are the main “secret killers” in poultry that lead to chronic oxidative stress and inflammation, which in turn impact the health and animal performance. Additionally, chronic stress in poultry is linked with the emergence of antimicrobial resistance (AMR), which the WHO has recently identified to be among the most important problems threatening human health globally that increased the demand for safe antimicrobials to treat the collateral damages resulting from dysbiosis. Several alternative feed additives such as probiotics, prebiotics, fatty acids, and amino acids have been described to restore intestinal microbiota. Additionally, some phytogenic substances have anti-inflammatory and antioxidant activities. These natural products are also capable to modulate gut microbiota in a symbiotic equilibrium, thereby enabling the intestinal tract to withstand both infectious and non-infectious stressors. Nevertheless, several challenges, such as the bioavailability, rate of absorption, quality inconsistency, public acceptance, and cost-effective delivery methods, make the feasibility and application of phytogenic substances on a commercial scale complicated. In this review, the main drivers of chronic inflammation in poultry have been discussed. Additionally, the potential use of alternatives to antibiotics to restore the gastrointestinal microbiota in poultry and the possibilities for overcoming breakdowns in poultry farming were highlighted