As agricultural production is reaching its limits regarding outputs and land use, the need to further improve crop yield is greater than ever. The limited translatability from in vitro lab results into more natural growth conditions in soil remains problematic. Although considerable progress has been made in developing soil-growth assays to tackle this bottleneck, the majority of these assays use pots or whole trays, making them not only space- and resource-intensive, but also hampering the individual treatment of plants. Therefore, we developed a flexible and compact screening system in which individual seedlings are grown in wells filled with soil. The combination of an insert plate, containing the wells, with an adapter plate, containing reservoirs, allows for single-plant irrigation, different liquid treatments and mimicking stress conditions. The system makes use of an automated image-analysis pipeline that extracts multiple growth parameters from individual seedlings over the time course of the experiment, including projected rosette area, relative growth rate, compactness, and stockiness. The system is also optimized for maize with results that are consistent with Arabidopsis while different in amplitude. We conclude that the PhenoWell® system enables the translation of results obtained from in vitro studies into useful applications in soil.