The valorization of fishery discards represents a key challenge for the sustainability of the maritime sector and the circular economy. This study evaluated the potential of whole European anchovy (Engraulis encrasicolus) from fishery discards as a nutritious and functional ingredient through its transformation into flour and its nutritional, functional, and microbiological characterization. Anchovies were processed by washing, grinding, autoclave sterilization (116 °C, F₀ = 6), drying, and milling to obtain a homogeneous flour. The resulting flour exhibited a high dry matter content (96.87%) and crude protein content (74.03%), together with a nutritionally balanced amino acid profile, with essential amino acids representing 50.59% of the total amino acid content and all indispensable amino acids meeting or exceeding the FAO/WHO/UNU reference amino acid pattern for adults. The flour also contained nutritionally relevant amounts of polyunsaturated fatty acids (4.73%), calcium (2.52%), and phosphorus (2.11%). Histamine concentrations were within acceptable limits, and microbiological analyses confirmed compliance with food safety criteria, with no detection of relevant pathogens. The results indicate that discarded anchovy flour has potential for incorporation into food and feed value chains, promoting the circular economy and the blue economy through a zero-waste-oriented strategy.