Optimizing fertilizer use in intensively cropped soils is essential, but knowledge of related issues among farmers is lacking. The present study assessed farmers’ perceptions of fertilizers and practices of fertilizer use in intensive cereal production in rural areas of Evros in northern Greece. In total, 250 cereal farmers were chosen for this study, and more than half of the farmers (53.6%) perceived that chemical fertilizers are hazardous, corroborating a general perception of chemophobia. Nevertheless, almost all farmers (98.8%) stated that they applied fertilization in their cereal production. Among them, 82.8% applied inorganic fertilizers, 9.2% applied green manure, 4.4% applied animal manure, and 3.6% applied commercial organic fertilizers. Most farmers used rates within the recommended rates in cereal production, while 12.9% and 6.2% of the farmers reported fertilization rates that were significantly lower or higher than those recommended for the area, respectively. Almost half of the farmers (48.8%) stated that they often use slow-release fertilizers and 30.8% stated that they frequently use foliar-applied fertilizers in cereals. Most farmers (57.2%) never kept records of annual fertilizations, while two-thirds of the farmers (66.4%) never asked for a soil analysis. Overall, most farmers (52.0%) showed traditional behavior, while only 5.2% showed innovative behavior in fertilizer use. Multiple regression analysis revealed that the innovative behavior was promoted by large-scale farmers, farmers who applied crop rotation, and farmers who perceived inorganic fertilizers as harmful. Moreover, large farm size and favorable attitudes concerning organic fertilizers were significantly associated with organic fertilizers use.