Food intake of the adult fruit fly Drosophila melanogaster, an intermittent feeder, is attributed to several behavioral elements including foraging, feeding initiation and termination, and food ingestion. Despite the development of various feeding assays in fruit flies, how each of these behavioral elements, particularly food ingestion, is regulated remains largely uncharacterized. To this end, we have developed a manual feeding (MAFE) assay that specifically measures food ingestion of an individual fly completely independent of the other behavioral elements. This assay reliably recapitulates the effects of known feeding modulators, and offers temporal resolution in the scale of seconds. Using this assay, we find that fruit flies can rapidly assess the nutritional value of sugars within 20-30 s, and increase the ingestion of nutritive sugars after prolonged periods of starvation. Two candidate nutrient sensors, SLC5A11 and Gr43a, are required for discriminating the nutritive sugars, D-glucose and D-fructose, from their non-nutritive enantiomers, respectively. This suggests that differential sensing mechanisms play a key role in determining food nutritional value. Taken together, our MAFE assay offers a platform to specifically examine the regulation of food ingestion with excellent temporal resolution, and identifies a fast-acting neural mechanism that assesses food nutritional value and modulates food intake.