The upper stems produce compound umbels of tiny yellow flowers. A typical umbel spans about 2-3" across, and consists of about 7-15 umbellets, which in turn have about 10-20 flowers. These flowers have short pedicels, except the central flower of each umbellet, which is sessile. Each flower has 5 yellow petals that barely open, and is less than 1/8" across. The blooming period occurs during late spring and lasts about a month. There is no noticeable floral scent.

Heartleaf Golden Alexanders differs from its close relative, Zizia aurea (Golden Alexanders), by its simple basal leaves, while the latter species has lower leaves that are compound.