In this paper, a disturbance observer is designed for the gust-load alleviation of a flexible high-altitude long-endurance (HALE) aircraft. A nonlinear dynamic model of a HALE vehicle is considered with a primary flight controller based on nonlinear dynamic inversion. Individual disturbance estimating filters (DEF) are designed to estimate and mitigate the effect of disturbances using sensor/actuator pairs of the aircraft. The individual DEFs are single-input single-output (SISO) disturbance observers for gust-load alleviation (DOGLAs) that are then combined together into a decoupled multi-input multi-output (D-MIMO) DOGLA. The D-MIMO DOGLA contains SISO DOGLAs dedicated to canceling out the effect of wind gusts on the body roll, pitch, and yaw rates of the aircraft, as well as on the deflection of the flexible wings. Numerical simulation results with the nonlinear flexible HALE aircraft model demonstrate that the D-MIMO DOGLA successfully mitigates the effect of wind gust loads on the aircraft in multiple flight profiles.