Aluminium (Al3+) is a non-essential metal ion and chronic exposure is considered toxic. Chronic Al3+ accumulation has been linked to cancers, neurodegenerative disorders such as Alzheimer’s disease, and is a major constraint to crop yield in acidic soil. Despite its insidious risks, aluminium compounds are constantly used in anti-perspirants, adjuvants, foods and beverages. Therefore, the fundamental insights into the mechanism of Al3+ toxicity need to be investigated. Through a genome-wide screen of the deletion mutants of Saccharomyces cerevisiae, we found protein kinase CK2 to be a key player in regulating Al3+ toxicity. CK2 is a highly conserved serine/threonine protein kinase consisting of two catalytic subunits and two regulatory subunits. Deletion of the catalytic subunit CKA2 provides resistance to Al3+. Five strains of S. cerevisiae (Al3+ sensitive BY4743, cka1Δ, ckb1Δ and ckb2Δ and Al3+ tolerant cka2Δ) were treated with 1.6mM Al3+ and H2O for the control in a growth time-course (0 to 16 hr) and performed in duplicate. Reverse phase chromatography was used for the creation of the spectral library, generated with ProteinPilotTM 5.0 and searched against the yeast Uniprot 2016 database, in which 3196 proteins (1% FDR) were identified. The generated data was imported into PeakViewTM 2.1 and matched against SWATH-MS data in which 2283 proteins were quantified. Statistical analysis of the differentially expressed proteins was performed using Perseus 1.5.5.3. In the Al3+ sensitive strains, Al3+ damages the cell wall, plasma membrane and disrupts the anti-oxidant response, which explains the sensitive phenotype of these strains. For Al3+ detoxification, the key findings of the protective role of cka2Δ against Al3+ include overexpression of proteins in sulfur metabolism, lysine biosynthesis and the heat shock response. These novel findings provide in-depth understanding of Al3+ toxicity and its detoxification, and have implications in finding solutions to Al3+-related problems in health and agriculture.