Obtaining proteins from agro-industrial by-products can enhance their value and reduce waste. Flaxseed meal, a by-product of flaxseed oil extraction, contains up to 40% protein. Enhancing flaxseed protein extraction and improving the functionality of the protein isolates presents an opportunity to add value to this by-product and to expand its application. This study aimed to optimize the alkaline extraction of proteins from flaxseed meal and to evaluate the impact of microfluidization on the physicochemical and techno-functional properties of the resulting protein isolates. Optimal extraction was achieved at pH 10.9 and 45 °C, with an extraction yield of 63.04% and a global yield of 29.71%. Microfluidization significantly reduced the particle size and β-sheet content while increasing the hydrophobicity, solubility, and α-helix content of flaxseed protein isolates (FPI). Additionally, there was a decrease in free-sulfhydryl groups as pressure increased. Concentrated FPI solutions exhibited gel-like behavior (G' > G”), with moduli increasing at 54 and 68 °C. Stability was maintained during frequency sweeps, and the highest-pressure treatment resulted in the lowest tan δ value, indicating more solid-like behavior. These findings underscore the potential of microfluidization as an industrial technique to enhance the functional properties of FPI obtained through alkaline extraction, particularly by reducing protein aggregation.