Although the consideration of socio-economic demands with biodiversity conservation is now high on the environmental policy agenda, it is not yet standard practice in spatial planning. This is argued to be related, among others, to a lack of awareness among stakeholders and practitioners of the underpinning role of ecosystem functioning and biodiversity to support human well-being. Meanwhile, there is mounting critique on the absolute focus of biodiversity conservation on static properties such as species and habitats. The establishment of more ecologically sensible objectives that include ecosystem processes besides species and habitats is put forward as a more effective way of environmental conservation. Methodological approaches increasingly consider ecosystem processes. However, the processes that are included mostly relate to aspects of biodiversity such as dispersal and productivity, and rarely do they include abiotic mechanisms that underlie biodiversity. We here report on the development of a method that integrates two principles which we identify as key to advance the integration of ecosystem services with biodiversity conservation in planning practice: (1) consider the variety of ecosystem processes, biotic as well as abiotic, that support biodiversity and ecosystem services, and (2) link the ecosystem processes to biodiversity and to socio-economic benefits to identify the common ground between seemingly conflicting objectives. The methodology uses a stepwise approach and is based on an extensive review of available knowledge on ecosystem functioning, expert consultation and stakeholder involvement. We illustrate how the methodology supports the setting of strategic goals to accomplish a healthy coastal ecosystem in Belgium, and exemplify how this may affect spatial plans. The aim of this paper is to demonstrate how including processes opens opportunities to align biodiversity and ecosystem services and how this increases chances to provide long-term benefits for biodiversity and human well-being. The paper may provide inspiration to advance current spatial planning approaches.