The ascent and temporary crustal storage of magmas beneath basaltic monogenetic volcanoes in continental settings is poorly understood, but is important in the study of their petrogenesis, and for monitoring future volcanic unrest. The Kaikohe-Bay of Islands volcanic field in northern New Zealand comprises Quaternary-aged monogenetic basalt volcanoes in an intraplate setting. Clinopyroxene phenocrysts in the basalts provide an opportunity to investigate the ascent history of the magmas that may not be evident from studies at the scale of whole-rock samples. The phenocrysts are texturally and compositionally diverse, and demonstrate the dominance of open system processes such as magma mixing and crystal entrainment in the crust. Many phenocrysts have an Mg (Mg# ~80–83) and Cr rich rim overgrowth which is in equilibrium with the host rock, but a resorbed, core (Mg# ~70) that crystallised from a more evolved magma. These crystals record mafic recharge, presumably the trigger to eruption. Other crystals are characterised by a high-Mg (Mg# ~82–84) and Cr core surrounded by a disequilibrium, low-Mg (Mg# 70–75) rim. The rims are reversely zoned and demonstrate late-stage equilibrium with the host rock. These crystals either nucleated in the host magma or were entrained from earlier basaltic intrusions of similar composition. The rim zones record re-melting of intrusions, or interaction with more differentiated magmas, followed by mafic recharge. Subordinate crystal types include oscillatory zoned crystals (Mg# >80) that nucleated in the ascending magma, and diffusely, patchy-zoned crystals that are variously antecrystic or xenocrystic in origin. Cognate gabbro inclusions contain clinopyroxene in equilibrium with the host basalt, suggesting they originated from side-wall crystallisation. Crystal-melt equilibria indicate that the cognate clinopyroxene formed at 430 ± 170 MPa (2σ) (=16 ± 6 km depth), and a subordinate population formed at 730 ± 160 MPa (=28 ± 6 km depth). These depths coincide with major seismic velocity contrasts at a zone of partial melt (10–19 km) and the Moho (~28 km). Thus, buoyancy or rheology contrasts in the crust temporarily slowed magma ascent and promoted periods of crystallisation and the assimilation of antecrystic and xenocrystic components. Similar magmatic processes occurred at the neighbouring and contemporaneous Whangarei volcanic field. Both of these fields have been active for millions of years, and longevity could explain the formation of differentiated crustal instrusives. In systems where magmas temporarily stall, there is a greater likelihood of detecting pre-eruption geophysical phenomena that could act as signals to pending eruptions.