AbstractCalcium/calmodulin‐dependent kinase II (CaMKII) is a key enzyme at the glutamatergic synapses. CAMK2A gene variants have been linked with alcohol use disorder (AUD) by an unknown mechanism. Here, we looked for the link between αCaMKII autophosphorylation and the AUD aetiology. Autophosphorylation‐deficient heterozygous αCaMKII mutant mice (T286A^+/−) were trained in the IntelliCages to test the role of αCaMKII activity in AUD‐related behaviours. The glutamatergic synapses morphology in CeA was studied in the animals drinking alcohol using 3D electron microscopy. We found that T286A^+/− mutants consumed less alcohol and were more sensitive to sedating effects of alcohol, as compared to wild‐type littermates (WT). After voluntary alcohol drinking, T286A^+/− mice had less excitatory synapses in the CeA, as compared to alcohol‐naive animals. This change correlated with alcohol consumption was not reversed after alcohol withdrawal and not observed in WT mice. Our study suggests that αCaMKII autophosphorylation affects alcohol consumption by controlling sedative effects of alcohol and preventing synaptic loss in the individuals drinking alcohol. This finding advances our understanding of the molecular processes that regulate alcohol dependence.