The variability of stable isotope ratios (δ²H, δ¹³C, δ¹⁵N, δ¹⁸O and δ³⁴S) along the production chain of pasta (durum wheat, flour and pasta) produced by using both conventional and organic farming systems in four Italian regions in 2 years was investigated. The aim was to evaluate if and how the farming system and geographical origin affect stable isotope ratios determined along the production chain. Irrespective of the processing technology, 65% of the samples were correctly classified according to the farming system and 98% were correctly classified regarding the geographical region. When considering both farming system and geographical region simultaneously, 80% of the samples were correctly classified. The measured isotope parameters were thus primarily affected by the geographical origin. In conclusion, it is expected that the use of these parameters will allow the development of analytical control procedures that can be used to check the geographical origin of Italian organic and conventional pasta and its raw materials.