This study aims to develop an integrated spatial planning methodology with a participatory planning approach for building resilient settlements against complex ecological risk factors. Düzce Province is selected as a case study because of its complex ecological characteristics as witnessed many times in past. The methodology consists of four phases. (1) The first phase of the methodology joins the ecological planning aims. In the (2) second phase, ecosystem services (ES) integrated land suitability maps was produced by combining natural hazard risks and landscape vulnerabilities with the risk of degradation of valuable ES. The (3) third phase, is participatory risk governance approach, which consists of three components namely, (a) risk communication, (b) risk assessment, (c) risk management that conducted between the local and regional stakeholders within the multi-scale approach. In the (4) fourth phase, comprehensive outputs for spatial risk mitigation was provided by the integration of ecological risk synthesis and participatory planning findings. Results show that participants prioritized earthquake, landslide, and flood as the highest natural hazard risks and erosion, habitat vulnerability, and water infiltration as the highest ecological vulnerability risks respectively. Results of risk governance analysis show that, at macroscale, central government institutions have the highest responsibility predominantly for proactive roles. At mesoscale local institutions of central governance have mainly reactive responsibilities. Thus, this integrated ecological risk assessment methodology can contribute to the decision-making process of ecological risk mitigation plans in a more comprehensive way through a multi-spatial and temporal scale approach. Moreover, this method can be applied in other provinces. However, in order to disseminate the results of participatory risk governance at provincial level, participation level and diversity should be increased in future studies.