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Monogenetic small-volume basaltic volcanoes are the most abundant subaerial volcanic landforms on Earth but are some of the most poorly understood systems. Their short durations, small volumes, and lack of recurrence make monitoring and hazard assessment difficult. The Zuni-Bandera volcanic field in western New Mexico contains small-volume basaltic centers erupting tholeiitic to alkalic basalts. Evidence shows no correlation of magma composition with eruption age, location, or volumetric output, prompting questions about the influence of magma ascent rates, magma storage conditions, and mantle source characteristics on lava compositions. Here, we present olivine major and minor element mineral chemistry from the 3200-year-old McCartys Flow, the youngest tholeiite basalt in the volcanic field. Olivine displays four phenocryst types with unique textures and major and minor element compositions. Multiple olivine types co-exist at the thin section scale. Major and minor element diffusion at frozen melt–phenocryst interfaces was modeled, revealing magma residence times ranging from 3–9 months. Type 3 olivine phenocrysts require step function initial conditions and record diffusion re-equilibration followed by magma mixing. These profiles indicate the magma resided in the reservoir for 10–15 years and accumulated from multiple batches of mixed magmas less than 10 days before the eruption. Our results show that primitive magmas in small-volume monogenetic volcanoes have complex lithospheric magmatic histories and stored in magma bodies influenced by an open system to develop different local chemical environments.