c. 1200, flour, also flur, flor, floer, floyer, flowre, "the blossom of a plant; a flowering plant," from Old French flor "flower, blossom; heyday, prime; fine flour; elite; innocence, virginity" (12c., Modern French fleur), from Latin florem (nominative flos) "flower" (source of Italian fiore, Spanish flor), from PIE root *bhel- (3) "to thrive, bloom."
From late 14c. in English as "blossoming time," also, figuratively, "prime of life, height of one's glory or prosperity, state of anything that may be likened to the flowering state of a plant." As "the best, the most excellent; the best of its or kind; embodiment of an ideal," early 13c. (of persons, mid-13c. of things); for example flour of milk "cream" (early 14c.); especially "wheat meal after bran and other coarse elements have been removed, the best part of wheat" (mid-13c.). Modern spelling and full differentiation from flour (n.) is from late 14c.
In the "blossom of a plant" sense it ousted its Old English cognate blostm (see blossom (n.)). Also used from Middle English as a symbol of transitoriness (early 14c.); "a beautiful woman" (c. 1300); "virginity" (early 14c.). Flower-box is from 1818. Flower-arrangement is from 1873. Flower child "gentle hippie" is from 1967.