An integration of geochemical and grain association studies were carried out on Middle Permian deposits in central Iran where both cool and warm water carbonates are found. The recrystallization of most bioclasts, lime-mud matrix and ooids along with high Sr contents suggests a probable original aragonite mineralogy for carbonates of the Middle Permian Jamal Formation at the Shotori section. Low bulk carbonate δ18O values imply pervasive diagenetic alteration in this section. Conversely, Middle Permian deposits at the correlative Bagh-e Vang section have a probable calcite precursor supported by low Sr contents and no evidence of recrystallization. This mineralogical variation in these coeval carbonates is considered to be due to the change in depth and temperature of the depositional palaeoenvironment. δ13C values started to rise over 2 ‰ PDB and reached a maximum of 4.3 ‰ PDB at the Wordian–Capitanian boundary at the Bagh-e Vang section. This δ13C rise is attributed to high primary productivity as previously reported in the Capitanian Abadeh Formation in central Iran. The positive δ13C excursion in these sections is correlated with the Capitanian ‘Kamura event’ identified from the mid-Panthalassian sections in Japan. No noticeable positive excursion occurs in the δ13C plot at the Shotori section making the interpretation of palaeo-productivity difficult. It is suggested that an active oceanic upwelling was the probable driver of the Middle Permian oceanic productivity in central Iran. Remarkable negative δ13C excursions around 3.7 and 4.2 ‰ PDB in Capitanian carbonates close to the Guadalupian–Lopingian boundary at the Bagh-e Vang and Abadeh sections, respectively are recorded, which are a proxy for low palaeo-productivity and a transition from a cool to warm climate, consistent with an early Lopingian sea level rise.