Protein kinase C βII (PKCβII) regulates diverse cellular signaling pathways involved in B-cell activation, insulin signaling, and oxidative stress-induced apoptosis. Aberrant PKCβII activity has been implicated in a variety of human diseases including diabetic retinopathy and B-cell immunodeficiency. Accordingly, PKCβII has become a popular target for small molecule based inhibition. However, the effects of available inhibitors on the conformational dynamics and allosteric couplings essential for PKCβII function remains largely unknown. This lack of knowledge hampers the development of improved inhibitors and limits our understanding of how disease-associated mutations in distal sites can interfere with inhibitor efficacy. Here we combine conventional and enhanced sampling molecular dynamics (MD) simulations with bioinformatics analysis to characterize distinct flexibilities and internal dynamical couplings upon inhibitor binding. MD simulations revealed increased flexibility of the nucleotide-binding P-loop and turn motif of the regulatory C-terminal tail when bound to the ATP-competitive inhibitor Bisindolylmaleimide I (BIM1). Dynamical cross-correlation analysis revealed variations between ATP and inhibitor states localized to the turn motif, P-loop, helix αE, and helices αG and αH of the GHI-subdomain. The ATP state displays stronger couplings between the turn motif and P-loop, as well as distinct couplings between active-site residues that are lost upon inhibitor binding. Furthermore, correlation network path analysis indicates that the inhibitor decouples the P-loop and catalytic loop from the turn motif. In addition, residues mediating distinct ligand-dependent couplings were identified in the C-terminal tail and N-lobe of the catalytic domain. Somatic mutations of a subset of these residues have been observed in cancer samples and the functional and structural dynamic effects of these mutations are currently been investigated.