The consumption of organically produced foods is gaining increasing popularity. Simultaneously, the areas under organic control are expanding. Data obtained from the Sentinel-2 satellite are exceptionally suitable for agricultural monitoring, as the mission provides data every 2–3 days, allowing for the tracking of changes in crops. Einkorn, known as the oldest wheat, finds wide application in various food products and is highly suitable for use in organic farming due to its resistance to weeds, various diseases, and pests. It is also highly suitable for crop rotation. In this study, we demonstrate the potential for monitoring yields of organic einkorn using Sentinel-2 satellite data. We tracked the development of the crop by selecting three different phenological phases: tillering, heading, and milk ripeness. We used images from these three phases, taken when we observed a mass entry of the crop into a given phase (minimum of 75% of plants in the crop in the respective phenological phase). Sampling sites were determined, with three different values of the Normalized Difference Vegetation Index (NDVI) established in the tillering stage: low, medium, and high. Upon reaching the technical ripeness phase, samples were taken in four replications at the three differences. Biometric measurements were taken, and the biological yield of the crop was determined. Correlation analysis was performed between ground-based yield data and Sentinel-2 satellite data. The study identified the phenological phases and vegetation indices most suitable for monitoring and predicting yields.