Increased ultraviolet-B (UV-B) due to global change can affect plant development and metabolism. Quinoa tolerates extreme conditions including high UV levels. However, the physiological mechanisms behind its abiotic stress tolerance are unclear, especially those related to UV-B. We previously demonstrated that 9.12 kJ m−2 d−1 may induce UV-B-specific signaling while 18.24 kJ m−2 d−1 promotes a UV-B-independent response. Here, we explored the effects of these UV-B doses on hormonal regulation linked to plant morphology and defense among diverse varieties. Changes in fluorescence parameters of photosystem II, flavonoids and hormones (indoleacetic acid (IAA), jasmonic acid (JA), abscisic acid (ABA) and salicylic acid (SA)) were surveyed under controlled conditions. Here, we showed that the sensitivity to short acute UV-B doses in varieties from different habitats is influenced by their parental lines and breeding time. UV-B sensitivity does not necessarily correlate with quinoa’s geographical distribution. The role of flavonoids in the UV-B response seems to be different depending on varieties. Moreover, we found that the extent of changes in JA and SA correlate with UV-B tolerance, while the increase of ABA was mainly related to UV-B stress.