Salmonellosis is still one of the most reported zoonoses worldwide and poultry meat is a major source, as chickens are often persistent carriers of Salmonella. Medium-chain fatty acids (MCFA) are known for their strong antimicrobial activity. MCFAs used today in the animal feed industry, however, mainly originate from the palm oil industry, which is notorious for its negative impact on the climate. We investigated the effect of a specific blend of palm-free MCFAs (ranging from C6 to C9) on Salmonella Enteritidis (SE) colonization in broiler chickens and in vitro SE characteristics. Fifty Ross 308 broiler chickens were randomly divided in 2 treatment groups. Chickens received either un-supplemented feed or feed supplemented with 300 ppm MCFAs from D0 onwards. On D7, all chickens were orally inoculated with 1600 CFU of SE. Cloacal swabs (D11) and samples of liver and caeca (D12) of all animals were collected and SE was enumerated. Percentage of SE-positive caecum samples was significantly (P = 0.044) reduced in birds receiving MCFAs compared to those receiving unsupplemented feed (36% vs. 64%). In vitro work performed with the same SE strain showed that preincubating the Salmonella bacteria with MCFAs at a sub-minimal inhibitory concentration significantly (p < 0.05) reduced bacterial adhesion to and invasion in Caco-2 cells, which may explain the observed reduction in intestinal SE colonization in the in vivo trial. Together, these results show that the tested eco-friendly MCFA blend could be a promising tool in the control of Salmonella in broilers.