Reported divergent responses of coral growth and skeletal microstructure to the nutrient environment complicate knowledge-based management of water quality in coral reefs. By re-evaluating published results considering the taxonomy of the studied corals and the N:P stoichiometry of their nutrient environment, we could resolve some of the major apparent contradictions. Our analysis suggests that Acroporids behave differently to several other common genera and show distinct responses to specific nutrient treatments. We hypothesised that both the concentrations of dissolved inorganic N and P in the water and their stoichiometry shape skeletal growth and microstructure. We tested this hypothesis by exposingAcropora polystomafragments to four nutrient treatments for > 10 weeks: high nitrate/high phosphate (HNHP), high nitrate/low phosphate (HNLP), low nitrate/high phosphate (LNHP) and low nitrate/low phosphate (LNLP). HNHP corals retained high zooxanthellae densities and their linear extension and calcification rates were up to ten times higher than in the other treatments. HNLP and LNLP corals bleached through loss of symbionts. The photochemical efficiency (Fv/Fm) of residual symbionts in HNLP corals was significantly reduced, indicating P-starvation. Micro-computed tomography (µCT) of the skeletal microstructure revealed that reduced linear extension in nutrient limited or nutrient starved conditions (HNLP, LNHP, LNLP) was associated with significant thickening of skeletal elements and reduced porosity. These changes can be explained by the strongly reduced linear extension rate in combination with a smaller reduction in the calcification rate. Studies using increased skeletal density as a proxy for past thermal bleaching events should consider that such an increase in density may also be associated with temperature-independent response to the nutrient environment. Furthermore, the taxonomy of corals and seawater N:P stoichiometry should be considered when analysing and managing the impacts of nutrient pollution.Supplementary InformationThe online version contains supplementary material available at 10.1007/s00338-022-02223-0.