Global fisheries production has increased up to ~200 MT, which has resulted in the intensive generation of waste or byproducts (~20 MT), which is creating serious problems for environmental management with zero income. This study proposes an idea of using whole fish (red and white meat, skin, bones, and fins but not scales) for human food (snack food) with the aim of zero waste generation. Whole fish powder (WFP) was prepared by a novel method (using freeze-drying as well as stone ball milling) and fortified in baked snacks at four levels (0, 5, 10, and 15% w/w of 100 g of formulation). The results revealed that the addition of WFP decreased expansion and color parameters compared to control. Hardness was significantly (p < 0.05) increased with the addition of WFP, which was attributed to the mineral content of WFP. Pasting properties determined by rapid visco analyzer (RVA) were dramatically decreased with the addition of 10–15% WFP, suggesting the weak interaction of starch and protein, which was also evidenced by scanning electron microscopy (SEM). Low field nuclear magnetic resonance (LF-NMR) analysis revealed that the amount of free water was increased when 10–15% WFP was added in snacks while bound water was highest in control and 5% WFP samples, respectively. The microstructural analysis by SEM showed that the protein network was increased in those samples incorporated with WFP compared to control that had more starch granules. The results suggest the feasibility of adding 5% WFP for proper structure, texture, pasting properties, and water distribution in order to reduce fish waste.