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The monolithic integration of sub-micron quartz structures on silicon substrates is a key issue for the future development of piezoelectric devices as prospective sensors with applications based on the operation in the high-frequency range. However, to date, it has not been possible to make existing quartz manufacturing methods compatible with integration on silicon and structuration by top-down lithographic techniques. Here, we report an unprecedented large-scale fabrication of ordered arrays of piezoelectric epitaxial quartz nanostructures on silicon substrates by the combination of soft-chemistry and three lithographic techniques: (i) laser interference lithography, (ii) soft nanoimprint lithography on Sr-doped SiO2 sol–gel thin films, and (iii) self-assembled SrCO3 nanoparticle reactive nanomasks. Epitaxial α-quartz nanopillars with different diameters (from 1 μm down to 50 nm) and heights (up to 2 μm) were obtained. This work demonstrates the complementarity of soft-chemistry and top-down lithographic techniques for the patterning of epitaxial quartz thin films on silicon while preserving its epitaxial crystallinity and piezoelectric properties. These results open up the opportunity to develop a cost-effective on-chip integration of nanostructured piezoelectric α-quartz MEMS with enhanced sensing properties of relevance in different fields of application., This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program, project SENSiSOFT (no. 803004); the French Agence Nationale pour la Recherche (ANR), project Q-NOSS ANR ANR-16-CE09-0006-01; the Spanish Ministry of Science Innovation and Universities in cofunding with European social funds through the Severo Ochoa Program for Centers of Excellence in R&D (SEV-2015-0496) and the Ramón y Cajal program (RyC-2012-11709 to J.G.); and the Generalitat de Catalunya (2017SGR00765). Q.Z. was financially supported by the China Scholarship Council (CSC) with no. 201506060170. Q.Z.’s work was done as a part of the PhD program in Materials Science at Universitat Autònoma de Barcelona. The authors thank the “Laboratorio de Microscopías Avanzadas-Instituto de Nanociencia de Aragón” for offering their expertise in the preparation of TEM cross sections. A. Crespi from XRD diffraction service is acknowledged for pole figure measurements. FEG-SEM instrumentation was facilitated by the Institut des Matériaux de Paris Centre (IMPC FR2482) and was funded by Sorbonne Université, CNRS and by the C’Nano projects of the Région Ile-de-France. We thank David Montero for performing the FEG-SEM images.