As loneliness is a risk factor for mental and physical health problems in various age groups, this study aimed to explore the impact of the intergenerational Shokuiku (food and nutrition education) program (IGSP) on loneliness in a Japanese community. This single-arm intervention study conducted between 2022 and 2023 included children (n = 21), guardians (n = 16), university students (n = 3), and older adults (n = 6). The IGSP was a one-day program that included participants making and eating their own bread, butter, and sorbet. Loneliness was measured using the Five-item Loneliness Scale for Children (Five-LSC; Japanese) and the three-item UCLA Loneliness Scale (Japanese; for adults) with other direct questions. Social capital, including civic participation, social cohesion, and reciprocity, was assessed using a self-administered questionnaire. The Five-LSC score significantly decreased post-intervention (p = 0.04). There was a significant increase in adults who reported not feeling lonely (p = 0.001). However, the UCLA Loneliness Scale scores did not show any significant changes. A positive change in social cohesion, including community contribution (p = 0.001) and attachment (p = 0.002), was observed among adults. This study suggests that IGSPs have a positive impact on loneliness in children and a partly positive one in adults. These findings emphasize the potential of intergenerational programs to reduce loneliness in communities.