The urban area is characterized by different urban ecosystems that interact with different institutional levels, including different stakeholders and decision-makers, such as public administrations and governments. This can create many institutional conflicts in planning and designing the urban space. It would arguably be ideal for an urban area to be planned like a socio-ecological system where the urban ecosystem and institutional levels interact with each other in a multi-scale analysis. This work embraces a planning process that aims at being applied to a multi-institutional level approach that is able to match different visions and stakeholders' needs, combining bottom-up and top-down participation approaches. At the urban scale, the use of this approach is sometimes criticized because it appears to increase conflicts between the different stakeholders. Starting from a case study in the Municipality of Lecce, South Italy, we apply a top-down and bottom-up participation approach to overcome conflicts at the institutional levels in the use of the urban space in the Plan of the Urban University Center. The bottom-up participation action analyzes the vision of people that frequent the urban context. After that, we share this vision in direct comparison with decision-makers to develop the planning and design solutions. The final result is a draft of the hypothetical Plan of the Urban University Center. In this way, the bottom-up and top-down approaches are useful to match the need of the community that uses the area with the vision of urban space development of decision-makers, reducing the conflicts that can arise between different institutional levels. In this study, it also emerges that the urban question is not green areas vs. new buildings, but it is important to focus on the social use of the space to develop human well-being. With the right transition of information and knowledge between different institutional levels, the bottom-up and top-down approaches help develop an operative effective transdisciplinary urban plan and design. Therefore, public participation with bottom-up and top-down approaches is not a tool to obtain maximum consensus, but mainly a moment of confrontation to better address social issues in urban planning and design.