A: You ate this. Have you brushed your teeth?
B: You ate this. Did you brush your teeth?
Sentence A is in the Simple Past, while B is in the Present Perfect.
Which sentence is more natural?
To me, the two sentences are equally natural, but express somewhat different ideas. The first, in the present perfect, means "Have you brushed your teeth since you ate it [i.e., at any time between then and now]?". The second, in the simple past, means "Did you brush your teeth after you ate it [i.e., in the past, soon after you ate it]?".