Rapidly and reliably elucidating the phases in polycrystalline materials is essential for developing new materials. Yet, crystals of many materials of biological, pharmaceutical, chemical, or industrial interest are too small (<1 μm) for routine X-ray diffraction (XRD) analysis. For complex materials, this can result in workflow bottlenecks in high-throughput synthesis screenings favoured by industrial laboratories. With the increased prevalence of electron diffraction as an alternative technique for materials characterization, we explore a series of zeolite syntheses, resulting in typical polycrystalline products, via high-throughput phase identification using serial rotation electron diffraction (SerialRED). Five zeolite phases were identified in one product, the most complex mixture ever discovered in zeolite chemistry. Some of the phases are of ultra-low contents, similar unit cells, and/or identical morphologies. Via automatically examining hundreds of crystals, SerialRED enables the reliable and high-throughput phase analysis of products that XRD could not handle. It allows the exploration of more complex synthesis systems and provides new opportunities for rapidly developing novel polycrystalline materials, greatly benefiting synthesis chemistry and material science.