In recent decades, due to the negative effects of conventional farming on human health and the environment, the organic farming is taken into consideration in order to produce healthy food materials. The aim of the present study was to assess the greenhouse owners’ knowledge, attitude, and practice with respect to healthy cucumber and tomato production in greenhouse farming systems in Isfahan county, Iran. Required data was collected on a sample of 110 farmers through face-to-face interviews based on a comprehensive structured questionnaire. Behavioral analysis of farmers’ decision making is based on “knowledge, attitude and practice” (KAP) survey using structural equation modeling. Research findings showed that despite the positive attitude of most greenhouse owners toward production of healthy crops, there is no proper use of pesticides and fertilizers in greenhouse farming. Although most farmers believe that overuse of pesticides and chemical fertilizers endangers human health and environment, but they don’t adhere to proper usage principles and amount of pesticides and chemical fertilizers. Also, small-scale greenhouses, weak farm economy, low literacy level, and lack of adequate awareness, have led to select the least risky and fastest way to combat the pests. Therefore, it is very important to improve greenhouse owners' knowledge in fertilizer selection and pest management, and strengthening the marketing system of healthy products.