This study characterised the Ser/Thr/Tyr phosphoproteome of classical Bordetella species and examined its role in Bordetella biology and virulence. This study found 70 unique phosphorylated proteins in the classical bordetellae group with a high degree of conservation observed and phosphorylation was a key regulator of Bordetella metabolism with proteins involved in gluconeogenesis, TCA cycle, amino acid and nucleotide synthesis significantly enriched. We also identified the phosphorylation of three key virulence pathways which separates classical from non-classical bordetellae including the type III secretion system, alcaligin synthesis (the primary siderophore produced by Bordetella) and the BvgAS master transcriptional regulatory system for virulence genes in Bordetella. Seven new phosphosites were identified in BvgA with 6 located in the DNA binding domain. Of the 7 new phosphosites, four were not detected in non-classical bordetellae. This suggests that serine/threonine phosphorylation may play an important role in stabilising or destabilising BvgA binding to DNA for fine-tuning of virulence gene expression and that BvgA phosphorylation may be an important factor that separates classical from non-classical bordetellae. This study provides the first insight into the phosphoproteome of classical Bordetella species and the role Ser/Thr/Tyr phosphorylation plays in Bordetella biology and virulence.