Techniques described herein are related to harmonizing the signaling of coding modes and filtering in video coding. In one example, a method of decoding video data is provided that includes decoding a first syntax element to determine whether PCM coding mode is used for one or more video blocks, wherein the PCM coding mode refers to a mode that codes pixel values as PCM samples. The method further includes decoding a second syntax element to determine whether in-loop filtering is applied to the one or more video blocks. Responsive to the first syntax element indicating that the PCM coding mode is used, the method further includes applying in-loop filtering to the one or more video blocks based at least in part on the second syntax element and decoding the one or more video blocks based at least in part on the first and second syntax elements.