The continued degradation of marine ecosystems, along with the ecosystem services they provide, suggest that new, innovative approaches are needed to scale up marine biodiversity protection and promote sustainable fishery practices. We synthesize information from Chile on the key processes involved in the development of alternative strategies for scaling up marine biodiversity conservation and discuss the complementarities with marine protected areas. Defined as “ancillary” marine conservation initiatives under the Convention of Biological Diversity, we suggest that these alternative strategies have the potential to capitalize on local stakeholders’ participation and contribute to solving livelihood and governance issues while playing a significant role in scaling up marine conservation. We specifically focus on two recent ancillary initiatives being piloted in Chile. The development of business model innovations which could enable biodiversity benefits from territorial user rights fisheries policies and the creation of municipal conservation areas. We identify how these initiatives could eventually help scale up marine conservation, discuss opportunities and challenges from these pilot experiences and conclude with the need for developing policy frameworks and cross-scale governance approaches which formally acknowledge marine ancillary conservation measures as part of an integrated way to manage marine biodiversity. Exploring and supporting alternative complementary marine conservation strategies is particularly relevant in Chile and Latin America, if biodiversity conservation initiatives are to scale in coverage, contribute to livelihood improvement of local communities, replenish fisheries and play key roles in adaptation to climate change.