Dietary amino acids are key determinants of lifespan and fecundity. Fruit flies achieve a balanced intake of amino acids under diverse physiological conditions by developing a protein-specific appetite. The Drosophila feeding motor program comprises behavioral modules (feeding bursts and activity bouts) which are tightly regulated by physiological states through feedback (e.g. nutrient deprivation) and feedforward (e.g. mating) mechanisms. Here, we aim to understand the neural-circuit mechanisms underlying physiological state-specific regulation of food intake by dissecting the functional and temporal relationships between protein deprivation and feeding as well as the underlying neural circuits. We discovered that there are temporal differences between regulating the frequency and the duration of feeding bursts, suggesting that distinct neuromodulatory mechanisms modulate these parameters. Different sensory neuron populations control frequency and duration of feeding bursts suggesting that distinct sensorimotor pathways regulate these feeding motor programs. We combined connectomics and trans-synaptic labeling to map neurons downstream of a group of gustatory receptor neurons (taste peg GRNs) that are important for sustaining feeding on proteinaceous food. High-resolution behavioral analysis and optogenetics confirmed the identity of a group of interneurons that specifically regulate the duration of feeding bursts in a nutrient-specific manner, suggesting different aspects of the feeding motor program are controlled by separate circuits.