Calendula officinalis is a useful model crop because calendula flowers are used both ornamentally and medicinally. Organic production systems have many challenges; among these is the synchrony of nitrogen mineralization with the requirements of the crop. Organic greenhouse substrates have significantly different initial nitrogen levels which influence the performance of calendula, the highest initial N and plant performance was found in the organic compost peat substrate (OCP). The addition of supplemental nitrogen improved performance, but only OCP performed as well as the conventionally fertilized peat-based substrate. The nitrogen mineralization patterns in a soil-based greenhouse pot experiment showed that highly processed amendments supplied the highest levels of nitrogen, and that these amendments showed greater vegetative growth when soil was amended with a high-input amendment, but flower production was reduced. There was no observed influence of water stress on nitrogen mineralization, but flowers from water stressed plants had approximately 50% higher concentrations of secondary compounds than non-stressed flowers. Nitrogen mineralization in organic production systems is difficult to predict, but highly influences plant productivity and performance.