The faintly scented flowers of Polystachya ottoniana grow on a short, drooping stem that becomes from 4 cm to 15 cm tall. Two to six flowers are produced per stem. Flower colour varies from yellowish cream to white.

The sepals become up to 13 mm long. The three-lobed, papillae-covered flower lip curls, a yellow line occurring along a ridge-like callus down its centre. There is a pink line on the two triangular lateral petals. Flower diameter is about 12 mm.

Flowering happens from late winter to early summer (Liltved and Johnson, 2012; Germishuizen and Fabian, 1982).