Faecal samples for 1,600 pigs were collected in a temperate farm, in a tropical farm, and during an acute heat stress (i.e. 3 weeks at 30 °C at 23 weeks of age) in the temperate farm, in a genetically connected design between all environments. The V3-V4 regions of the 16SRNA were sequenced and 1,688 operational taxonomic units (OTU) were obtained. All animals were genotyped with a 60K SNP-chip. Feed had the same nutritional composition between environments, and was identical in the two periods tested in the temperate farm. Earlier studies showed that feed intake was reduced in the tropical environment, as was growth rate and fatness, and some G×E were evidenced on these traits. Linear mixed models were used to run association studies in each environment at the level of OTU and at different taxonomic levels. About 10% of the OTU had heritability close to zero in one of the environments and higher than 0.2 in another environment. In addition, associations between SNPs and some microbiota components were identified: which most strongly differed between the three environments. Altogether, our results suggest different genomic control of the faecal microbiota composition of growing pigs in temperate, acute heat stress and tropical chronic heat stress conditions. These potential G×E on microbiota could result from different feed resources, feed intake or other parameters directly related to breeding environment differences. They question the potential of selection for microbiota composition given the large range of changing environments in which pigs are now produced worldwide. This study is part of the Feed-a-Gene Project, funded from the European Union’s H2020 Programme under grant agreement no 633531.