After a period of vegetative growth, plants undergo a developmental switch to the reproductive phase, inducing the transition to bolting, elongation of the inflorescence and flowering. We have identified calcium-dependent protein kinase CPK28 from Arabidopsis thaliana as a regulatory component that controls stem elongation and vascular development. In two independent mutant alleles of cpk28, a reduction of stem elongation, accompanied by shorter leaf petioles and enhanced anthocyanin levels, is observed upon the transition to the generative phase. Anatomical analysis revealed an altered vascular pattern characterised by fewer xylem tracheary elements but at the same time increased lignification and secondary growth. Coincident with these morphological changes, cpk28 mutants showed altered expression of NAC transcriptional regulators NST1 and NST3 as well as of GA3ox1, a key regulator of gibberellic acid homeostasis. In vitro protein kinase activity of CPK28 is strictly calcium-dependent. Furthermore, CPK28 is phosphorylated in vivo at several sites. Site-specific amino acid substitutions at these phosphorylation sites resulted in reduced in vitro activity. However, when introduced into a cpk28 mutant background, wild-type and phosphorylation site variants, but not kinase-inactive variants of CPK28 complemented the morphological and developmental defects. Our data identify CPK28 as a developmentally controlled regulator for coordinated stem elongation and secondary growth.