This study aimed to analyze how perceptions of eco-friendly agricultural products affect food choice criteria, based on a sample of 225 study participants (consumers) in Sejong City, South Korea. We focused on the following criteria: Health, food safety, environmental protection, trust, reputation, nutrition, and taste. We used factor analysis to classify responses into three types of consumer attitude: Organic-minded, pesticide-free focused, and local food-minded. Then, we applied a logit analysis to determine values of agricultural products (dependent variables) and consumer attitudes toward eco-friendly agricultural products (independent variables). We found that South Korean consumers were not motivated by health or environmental protection, nor were they substantially concerned about food safety; their utmost concern was the reputation of organic products. Pesticide-free focused and local food-minded consumers placed a higher value on nutrition and taste, respectively, likely because, in South Korea, organic agriculture is a component of eco-friendly agriculture, leading to the entanglement in consumer perceptions of organic and pesticide-free products. This paper discusses how phased development strategies of organic agriculture, including the eco-friendly agricultural policy, have failed. It is therefore needed to develop and implement new policies for South Korean eco-friendly agriculture.