Salmonella has been recognized as one of the most important zoonotic pathogens worldwide, being poultry derived products the main source of human infection. Among the most promising tools for Salmonella control at the field level in poultry production are included bacteriophages (or phages). However, little is known about the phage application impact on the rest of the gut microbiota. In this sense, new studies suggest that phage application may affects the gastrointestinal ecology homeostasis. Therefore, the general objective of this doctoral thesis was to apply bacteriophages for Salmonella control in broiler production, focusing on their effect on intestinal health, by means of genomic sequencing and metabolomic study. To achieve this goal, two different parts were performed. The first part studied the phage gastrointestinal dynamics in Salmonella-free broilers and its influence on microbiota and metabolome, meanwhile the second part studied the phage dynamics in Salmonella-infected broilers and its influence on microbiota and metabolome. The results aim to provide important insights into the use of phages as a preventative and biocontrol strategy against Salmonella infection from farm-to-fork.