Most rhyolite eruption episodes of Tarawera volcano have emitted several physiochemically distinct magma batches (∼1–10 km3). These episodes were separated on a millennial timescale. The magma batches were relatively homogeneous in temperature and composition at pumice scale (>4 cm), but experienced isolated crystallisation histories. At the sub-cm scale, matrix glasses have trace element compositions (Sr, Ba, Rb) that vary by factors up to 2.5, indicating incomplete mixing of separate melts. Some quartz-hosted melt inclusions are depleted in compatible trace elements (Sr, Ti, Ba) compared to enclosing matrix glasses. This could reflect re-melting of felsic crystals deeper in the crystal pile. Individual quartz crystals display a variety of cathodoluminescence brightness and Ti zoning patterns including rapid changes in melt chemistry and/or temperature (∼50–100°C), and point to multi-cycle crystallisation histories. The Tarawera magma system consisted of a crystal-rich mass containing waxing and waning melt pockets that were periodically recharged by silicic melts driven by basaltic intrusion.