In egg production environments, many bacterial species co-exist on surfaces and equipment which can act as reservoirs of microbial contamination. Within these consortia, some bacteria have the potential to influence the growth and survival of pathogenic bacteria such as Salmonella enterica. When grown in co-culture with Acinetobacter johnsonii, Salmonella enterica has been found to have significantly higher tolerance to benzalkonium chloride compared to single culture. In this study, a dual RNA-seq analysis of S. enterica and A. johnsonii, both previously isolated from an egg farm, was conducted to elucidate the S. enterica genes induced by co-culture in a colony biofilm at 25 °C for 20 h. We found 700 genes to be differentially expressed, including 405 up-regulated and 295 down-regulated genes. Gene ontology enrichment analysis revealed that lipid A biosynthesis, iron transport and anaerobic respiration were up-regulated, while flagellum/motility, aerobic respiration and lipid catabolism was down-regulated. Interestingly, KEGG pathway analysis found that three pathways involved in lipid A modification and associated with cationic antimicrobial peptide resistance (CAMP), were up-regulated in S. enterica grown in co-culture. Specifically, pagP and pmrD genes of the PhoP-PhoQ two-component system and the PmrAB controlled arn (pmr) regulon were significantly overexpressed (p < 0.01). The PmrAB regulated eptA gene, conferring phosphoethanolamine transferase, was also up-regulated. Collectively, these gene pathways increase resistance to CAMP by reducing the net negative charge of Lipid A, decreasing the affinity of cationic antimicrobials. Point mutations to pmrB and overexpression of the PmrAB regulon have previously been associated with increased benzalkonium chloride tolerance and polymyxin resistance in S. enterica. This work highlights the importance of inter-species interactions, which can influence the efficacy of benzalkonium chloride. The results expand the knowledge of mixed-species culture and may help inform effective strategies to eliminate S. enterica in the egg production environment.