The acetylation of lysine residues in histones are an important regulatory mechanism. But still relatively little is known about the dynamics of histone acetylation and their dependency on metabolic processes. We therefore developed a stable isotope labelling approach based on ^13^C-glucose that allows the quantitative analysis of histone acetylation dynamics in human cell lines. The substrate for histone acetylation is acetyl-CoA which first needs to be synthesized from ^13^C-glucose causing a delay in the label incorporation of histone-acetyl-lysins. To correctly determine histone-acetylation dynamics we therefore simultaneously extracted proteins and metabolites and measured the time-dependent incorporation of ^13^C into both acetyl-CoA and acetylated histone peptides. We than used an ODE based modelling approach to calculate the correct histone acetylation and deacetylation rates. We show that without correction alterations in metabolic fluxes would erroneously be interpreted as changes in histone acetylation dynamics while our approach allows to discriminate between both processes.