As with most other stramenopiles, the anterior flagellum bears two rows of tripartite tubular hairs. The presence of three terminal fibrils, the central one longer than the two on the sides, helps distinguish Cafeteria from other naked stramenopile flagellates.

The cells are uninucleate. There is a single Golgi body anterior to the nucleus and near the flagellar bases. About five sausage-shaped mitochondria are present; as in other stramenopiles, the cristae are tubular.

Ejectile organelles (extrusomes) with a characteristic pattern dot the surface of the cell, especially in the vicinity of the cytostome.

The cytoskeleton is based on an asymmetrical system of two flagellar bases, three microtubular roots, and a forked rhizoplast. One of the three microtubular roots arises from the anterior basal body, and has secondary cytoskeletal microtubules associated with it; this is a common feature among stramenopiles. The other two microtubular roots arise from the posterior basal body.

The broader (12 microtubules) of these two roots is subdivided distally into three subunits that, together, define the feeding basket or cytostome.

The feeding basket is displaced to the right of the axis defined by the posterior basal body and flagellum. This feature, plus the lack of an overlap between the distal ends of the two roots arising from the posterior basal body, help separate bicosoecids from other naked stramenopile flagellates, especially the colorless chrysophytes Paraphysomonas and Spumella.