We present multi-epoch Very Large Telescope/Spectro-Polarimetric High-contrast Exoplanet REsearch observations of the protoplanetary disk around HD 135344B (SAO 206462). The J-band scattered light imagery reveal, with high spatial resolution (∼41 mas, 6.4 au), the disk surface beyond ∼20 au. Temporal variations are identified in the azimuthal brightness distributions of all epochs, presumably related to the asymmetrically shading dust distribution in the inner disk. These shadows manifest themselves as narrow lanes, cast by localized density enhancements, and broader features which possibly trace the larger scale dynamics of the inner disk. We acquired visible and near-infrared photometry which shows variations up to 10% in the JHK bands, possibly correlated with the presence of the shadows. Analysis of archival Very Large Telescope Interferometer/PIONIER H-band visibilities constrain the orientation of the inner disk to i = 18.• 2
+3.4−4.1 and PA = 57.• 3 ± 5.• 7, consistent with an alignment with the outer disk or a minor disk warp of several degrees. The latter scenario could explain the broad, quasi-stationary shadowing in N-NW direction in case the inclination of the outer disk is slightly larger. The correlation between the shadowing and the near-infrared excess is quantified with a grid of radiative transfer models. The variability of the scattered light contrast requires extended variations in the inner disk atmosphere (H/r 0.2). Possible mechanisms that may cause asymmetric variations in the optical depth (∆τ 1) through the atmosphere of the inner disk include turbulent fluctuations, planetesimal collisions, or a dusty disk wind, possibly enhanced by a minor disk warp. A fine temporal sampling is required to follow day-to-day changes of the shadow patterns which may be a face-on variant of the UX Orionis phenomenon.