Cultivation of buckwheat (Fagopyrum esculentum Moench) under Mediterranean photothermal conditions could affect synthesis of the flavonoid rutin and its partitioning within the plant, thus affecting the nutraceutical value of plant products. We examined rutin concentration and yield in the forage and the grain of common buckwheat grown under Mediterranean field conditions, in response to sowing time, irrigation, growth stage at harvest, and variety. The highest rutin concentration and yield in the forage were obtained with late spring sowing, thanks to greater accumulation of solar radiation and higher efficiency of rutin synthesis per photothermal unit. Water supply promoted a more efficient use of light resources for both biomass accumulation and rutin synthesis. Rainfed conditions reduced biomass accumulation to a greater extent than rutin synthesis. Rutin concentration was highest in leaves, followed by inflorescences, stems and achenes, and in all plant parts it decreased with plant age. In the grain, rutin concentration was highest with late spring sowing, and rutin yield was highest with early spring sowing. Correlation analyses suggest that rutin synthesis proceeds from the leaves to the other plant parts. Our research demonstrates that buckwheat can be cultivated in Mediterranean regions as a source of rutin for medicine and for food and feed supplementation.