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Many experimental studies have addressed the crystallisation of zircon, not least because zircon is of paramount importance as a geochronometer. Today, it is well established at what temperature, melt composition, and Zr concentration a silicate melt reaches zircon saturation. It remains unclear though what course a Zr bearing melt takes before zircon appears as a macroscopic phase. Does zircon nucleate directly from the melt, or does it use during nucleation and growth Zr-rich nanoparticles as fundamental building blocks? The question is relevant because Zr4+ is a high field strength (HFS) cation that should tend to polymerise in silicate melts to (ZrO2)n clusters. To fill that gap of knowledge, we performed experiments with a Zr-enriched phonolitic melt at 1200 (outside zircon stability) and 900° C (inside zircon stability). We investigated the glasses with Transmission Electron Microscopy (TEM) and Atom Probe Tomography (APT) for Zr-rich nanoparticles, at a spatial resolution not achieved by previous experiments involving zircon. A wide range of nanoparticles is identified, including baddeleyite, zircon, zirconium titanate ZrTiO4, and rutile. The diverse range of nanoparticles is probably owed to the fact that local-scale gradients in silica (aSiO2) among silicate melt pools prevailed despite the high run temperatures. The smallest and presumably earliest phases are (ZrO2)n nanoparticles trapped by liquidus corundum. They reach diameters around 2 nm or ~ 200 unit cells if they are crystalline. The results support the assumption that Zr4+ dissolves in silicate melts as ZrO2 monomers, then quickly polymerises to (ZrO2)n clusters. The same may be valid for other HFS cations. Possible applications to HFS element depletions in arc basalts are discussed. At 900° C inside zircon stability, many examples are noted where zircon grows by peritectic reaction of baddeleyite nanoparticles with SiO2 of the melt although zircon nanoparticles also exist. Larger baddeleyite grains around 50 nm seem to grow by aggregation of smaller (ZrO2)n nanoparticles. That zircon also grows by particle attachment cannot be confirmed. Zircon can also crystallise directly from the melt when in melt pools the aSiO2 and Zr contents were high enough to stabilise zircon.