For low-mass stars (M < 1.4 M☉), the connection between stellar rotation and magnetic activity governs stellar spin-down, shapes the environments and habitability of their exoplanets, and provides an age-diagnostic via magneto-gyro-chronology. Recently, an unexpected phenomenon known as the 'rotational stalling' was discovered, where stars rotate more rapidly than predicted, likely due to internal angular momentum redistribution. This rotational feature has been shown to cause enhanced magnetic activity on the photosphere, as measured by the photometric index from stellar light curves (Sph). However, the influence of the rotational stalling on other magnetic activity proxies has not been explored in depth. In this work, we study the impact of the rotational stalling on chromospheric magnetic activity proxies, namely the CaII-infrared triplet (IRT) index and the near-ultraviolet (NUV) excess. We target the stars observed by the Kepler mission, as this is the largest and most reliable sample with rotation period measurements. We calculate the CaII-IRT and NUV indices for the Kepler stars using data from the Gaia and GALEX missions, respectively. We study the rotation-activity relation as a function of Hertzsprung-Russell (HR) diagram location and spectral type, finding that K-dwarfs are more active than G-dwarfs. Importantly, we find that for main-sequence stars, chromospheric magnetic activity is also enhanced by the rotational stalling, mirroring its effect on the photospheric index Sph. Our work reveals that the rotational stalling marks a genuine transition in stellar magnetic behavior. This highlights the need to account for its multi-wavelength signatures across activity proxies, its impact on exoplanet habitability, and its consequences for age-rotation-activity relations.