Pistachio (Pistacia vera L.) cultivation under rainfed conditions of the South Mediterranean has not been studied in depth. Under changing climate conditions, knowledge of cultivar and rootstock performances allows for the optimal use of genetic resources to improve yield and nut quality. This study aimed to evaluate growth, yield, and fruit characteristics of ‘Mateur’ and ‘Achouri’ pistachio cultivars grafted on P. vera and P. atlantica rootstocks grown in northeastern Tunisia. The research was based on three years worth of monitoring of growth, yield and fruit quality. Results showed that annual bio-climatic features had significant effects on all studied parameters. The ‘Mateur’ cultivar showed higher vigor and fruit yield than ‘Achouri’. Fruit production was higher in P. atlantica rootstock for ‘Mateur’ but similar in both studied rootstocks for ‘Achouri’. Kernel fat contents (40.7–46.8%) and fatty acid profiles were low or not affected by cultivar, rootstock and their combination. Oleic acid (C18:1) was the major fatty acid (68.94–69.22%) in kernel oil. The unsaturated/saturated fatty acid and oleic/linoleic acid ratios indicated that nuts obtained had high quality. The lower performances of ‘Achouri’ cultivar in the studied conditions may be related to low acclimation ability of this cultivar. These conditions, however, seem to be suitable for both studied rootstocks.