- In recent years, the Israeli wheat industry has suffered from quality problems that can endanger the possibility of using the wheat to produce bread. The aim of this study is to understand how climatic and management factors, such as N fertilization, emergence date and wheat cultivar, affect the Gluten Index (GI) – a main wheat quality parameter in the Israeli commercial market. The study was undertaken at individual producer fields across southern Israel on three different scales: regional, farm, and the field. Overall, 1800 samples of 15 genotypes were collected, over three consecutive seasons, 2006–2008, from commercial fields throughout the area, from experiments conducted in the fields of the Gilat Research Center, and in the fields of Kibbutz Sa’ad. Climatic variables were mapped exclusively and on the basis of maximum temperature and rainfall data, and were collected in the course of the entire season and during certain periods. Relationships between climatic variables and GI were determined by multivariate regression analyses. On regional scale, the ability of explaining the differences was low, while on the farm and field scale, variation explanation was generally higher. The factors that were found to be most influential on wheat quality in southern Israel are: (1) type of variety; (2) negative influence of cumulative temperature stress; (3) negative influence of excess water; and (4) negative influence of excess nitrogen fertilization. It was found that the genotype is the most important factor influencing GI, but environmental and crop management factors also have a strong effect on the frequency and severity of GI depreciation. The probability of GI reduction increases in “too good” (excess fertilization, redundant irrigation) and in “too bad” conditions (water and temperature stress). Hence, when farmers make decisions regarding sowing, applying nitrogen and/or supplemental irrigation, they must also consider quality parameters, such as GI and not only yield quantity.