Background <p>Shapefiles are a geospatial vector data format used to indicate geographic features in geographic information systems (GIS) software. Shapefiles are used in high-throughput phenotyping plant breeding and agronomic studies to identify plots from aerial imagery and extract remote sensing data. However, the process of manually creating shapefiles is tedious and error prone. Current options that assist in shapefile generation suffer from issues such as installation processes that require a degree of programming knowledge or inefficient methods for incorporating plot-level information from field books. In this study, we have developed a program called ‘SHP Buddy’, a QGIS plugin that provides accessible and intuitive functions that quickly generate shapefiles for common experimental layouts used in agricultural research.</p> Results <p>SHP Buddy is a free and open source QGIS plugin that is easily downloaded directly from the QGIS plugin repository. It provides options for generating serpentine replicated and unreplicated experimental layouts. Further, SHP Buddy is the first of its type to provide an intuitive method for removing non-experimental plots, such as non-experimental “fill” plots at the end of experiments or plots in irrigation wheel tracks. Plot information is easily incorporated by uploading a field book CSV file that contains a column of matching plot numbers. Lastly, plot dimensions can be modified to produce more precise regions of interest.</p> Conclusions <p>SHP Buddy substantially reduces the time and increases the accuracy of shapefile generation. This results in reliable shapefiles that improve record keeping and the quality of high-throughput phenotyping data extracted. By working natively in QGIS, SHP Buddy provides an efficient solution to shapefile generation while maintaining a low learning curve.</p>