The chicken gastrointestinal tract is richly populated by commensal bacteria that fulfil various beneficial roles for the host, including helping to protect from colonisation by pathogens. However, this environment can also serve as a milieu that permits the conjugative transfer of plasmids between bacteria. The exchange of multidrug resistance plasmids between commensal and pathogenic bacteria is a significant public and animal health concern. Using an in vitro chemostat system to culture the chicken caecal microbiota, we simulated pathogen colonisation and examined the dynamics of plasmid transfer by inoculation with a strain of Salmonella serovar Typhimurium harbouring an IncI1 plasmid encoding multidrug resistance, including the Extended-Spectrum Beta-Lactamase gene blaCTX-M1. We also evaluated the impact of cefotaxime administration on plasmid transfer and the microbiota. Bacterial population community profiles were obtained by amplification and 454 pyrosequencing sequencing of the 16S rRNA gene. Salmonella inoculation resulted in no significant changes to community alpha and beta diversity whereas administration of cefotaxime caused significant alterations to both; reflecting findings from in vivo studies. Transfer of the multidrug resistance plasmid from Salmonella to commensal Escherichia coli was demonstrated by PCR and whole genome sequencing of representative isolates recovered from agar plates containing cefotaxime. Transfer occurred to seven sequence types of commensal E. coli at high rates, even in the absence of cefotaxime administration, with resistant E. coli being recovered within three days. Therefore the chemostat system developed provides an in vitro environment to model bacterial interactions, including transfer of antibiotic resistance, which closely simulates that found in vivo and which can be used to inform risk models of dissemination of antibiotic resistance through the food chain. In future, this system can be used to assess and refine interventions that may serve to mitigate the spread of antibiotic resistance before employing costly in vivo studies in higher animals.