The flowers of Polygala amatymbica grow solitary or in small clusters from leaf axils.

The flowers are bright magenta or blue-purple. Two rounded, petal-like sepals form the brightly coloured wings, while the petals are reduced, apart from the keel that ends in the brush-like crest. The plant is variable in flower size and colour.

Flowering happens in spring and sometimes or in some places summer as well (Pooley, 1998; Van Wyk and Malan, 1997; Germishuizen and Fabian, 1982; iNaturalist).