Recently, ether lipids have been introduced as long-term stable alternatives to the more natural, albeit easier degradable, ester lipids in the preparation of oriented lipid bilayers and bicelles for oriented-sample solid-state NMR spectroscopy. Here we report that ether lipids such as the frequently used 14-O-PC (1,2-di-O-tetradecyl-sn-glycero-3-phosphocholine) may induce significant changes in the structure and dynamics, including altered interaction between peptides and lipids relative to what is observed with the more conventionally used DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine) bilayers. Such effects are demonstrated for the antimicrobial peptide novicidin, for which 2D separate-local-field NMR and circular dichroism experiments reveal significant structural/conformational differences for the peptide in the two different lipid systems. Likewise, we observe altered secondary structure and different temperature-dependent membrane anchoring for the antimicrobial peptide alamethicin depending on whether the peptide is reconstituted into ester or ether lipids. Such observations are not particularly surprising considering the significant difference of the lipids in the phosphorus headgroup and they may provide important new insight into the delicate peptide-membrane interactions in the systems studied. In contrast, these observations reinforce the need to carefully consider potential structural changes in addition to long-term stability prior to the selection of membrane environment of membrane proteins in the analysis of their structure and dynamics. In more general terms, the results underscore the necessity in structural biology to address both the protein and its environments in studies relating structure to function.