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Active power filter (APF) control is a natural area of application for vibrating reference frame (VRF) transformation due to the intentional occurrence of higher harmonics in the active filter current compensating load current harmonics. Due to the vibrating frame transformation, the APF current can be represented by the DC values, and thus proportional-integral (PI) controllers are sufficient to control the converter current. However, in the typical approach, it may be impossible to combine harmonic filtration with reactive power compensation features, due to the transformation constraints. The solution to this issue is decoupling of the fundamental harmonic and high harmonic components and a separate control for each of them. This paper presents a decoupled control system of an APF, which uses VRF transformation for accurate control of high-current harmonics. Decoupling is a groundbreaking improvement of the VRF method. Moreover, different current limitation scenarios are proposed, considering both harmonics compensation and fundamental frequency reactive current compensation. Theoretical considerations are supported by simulation and experimental tests.