This disclosure relates to heading misalignment estimation with a portable device and more specifically to estimating misalignment between a portable device having a sensor assembly and a platform transporting the portable device when the platform is undergoing motion having periodic characteristics. In one aspect, a suitable method includes obtaining inertial sensor data for the portable device and determining an effective frequency characteristic of the inertial sensor data representing the motion having periodic characteristics. The inertial sensor data may be processed using the determined frequency characteristic so that a heading misalignment may be estimated between the heading of the portable device and the platform.