Premature ripening (PR) is one of the most important diseases of sunflower in France since the 90s. Previous results indicated that girdling canker of the stem base, caused by Phoma macdonaldii was its primary cause but elucidation of critical environmental factors involved is crucial for better control of the disease. A field study was conducted in three contrasting cropping seasons (2006–2008) and investigated the effect of N fertilization (0, 75 and 150 kg N ha−1) and water regime (rainfed, irrigated) on two cultivars with artificial inoculation (AI) and natural infection (NI). Disease assessment was recorded weekly to calculate the area under disease progress curve (AUDPC) and the final percentage of PR plants. Data showed that high levels of N fertilization led to significantly (P < 0.05) more PR than non-fertilization. Water deficit conditions were significantly (P < 0.05) involved in disease severity, and AUDPC and PR were increased when dry conditions were associated with high N supply. This was true for two cultivars which differed in their susceptibility to the disease but cv. Heliasol RM was significantly (P < 0.05) more affected than cv. Melody, partially resistant to PR. Despite contrasting weather patterns, these results demonstrated a clear role of crop management and environmental conditions on the incidence and severity of stem base attacks responsible for the PR syndrome. These findings suggest that sunflower crop husbandry should be adapted to minimize premature ripening induced by P. macdonaldii.