The grapevine (Vitis vinifera) is one of the most significant fruits in global economy, today as in the past. The international modern wine industry, traditional agriculture and wild populations encompass thousands of grapevine varieties, the differences between them often imperceptible to the naked eye and therefore, necessitating the application of digital technologies. This study aimed at establishing a methodology for analyzing grapevine pips using a 3D scanner, including an optimal protocol for removing the pips’ tissue to improve the botanical identification of recent and ancient specimens. The study presents mechanical, chemical and biochemical methods used to prepare the pips for scanning, the sample including 1400 modern grapevine pips belonging to 91 varieties and 300 grape pips from archaeological sites. In addition, several methodological tests were conducted to assess the tool’s sensitivity to positioning errors and possible morphological changes during natural ancient desiccation. Our study demonstrates the potential of this methodology for archaeological research and its implications for the wine industry.