Incorporation of the histone variant H2A.Z into nucleosomes by the SWR1 chromatin remodelling complex is a critical step in eukaryotic gene regulation. In Arabidopsis SWR1c and H2A.Z have been shown to control gene expression underlying development and environmental responses. Although they have been implicated in defense, the specific roles of the complex subunits and H2A.Z in immunity are not well understood. In this study we analysed the role of the SWR1c subunits, PHOTOPERIOD-INDEPENDENT EARLY FLOWERING1 (PIE1), ACTIN-RELATED PROTEIN6 (ARP6), and SWR1 COMPLEX 6 (SWC6), as well as H2A.Z, in defense and gene regulation using mutant analysis. We found that SWR1c components play different roles in resistance to different pathogens. Loss of PIE1 and SWC6 as well as depletion of H2A.Z led to reduced basal resistance while loss of ARP6 resulted in enhanced resistance. We found that mutations in PIE1 and SWC6 result in impaired effector-triggered immunity. Mutation in SWR1c components and H2A.Z also resulted in compromised JA/ET-mediated immunity. Genome wide expression analyses similarly reveal distinct roles for H2A.Z and SWR1c components in gene regulation, and suggest a potential role for PIE1 in the regulation of the cross talk between defense signaling pathways. Our data show that although they are part of the same complex, Arabidopsis SWR1c components could have non-redundant functions in plant immunity and gene regulation.