An unexpected retention order for the ketamine analogs methoxpropamine (MXPr) and methoxisopropamine (MXiPr) was observed when using a biphenyl stationary phase for liquid chromatography-mass spectrometry (LC–MS). For separations of isomeric pairs of drugs (ketamine analogs, tryptamines, fentanyls, and nitazenes), branched-chain compounds are eluted before straight-chain compounds when using acetonitrile or methanol in mobile phases with C18 or biphenyl stationary phases. However, when a biphenyl stationary phase was paired with methanol, the opposite retention order for MXPr and MXiPr occurred, which was not observed when using acetonitrile in the mobile phase. The phenomenon persisted in biphenyl columns from two vendors. This study suggests additional work may be needed to understand the retention mechanisms when using biphenyl stationary phases. It is an example that we can still expect the unexpected when investigating alternative stationary phases of reversed-phase liquid chromatography (RPLC).