The implementation of eco-innovations can be a strategy to combine economic benefit and reduce negative environmental impact. German greenhouse production is highly energy intensive, as heating and energy account for the second largest cost factor. Thus, the sector wants to develop and implement eco-innovations to speed up the process towards increased sustainability. In this paper, a sectoral systems of innovation (SSI) analysis is presented to identify and describe interrelated systemic barriers for developing and implementing such innovations into the sector. The SSI was used as an analytical framework, which enabled covering different system levels and components in the research in order to draw a comprehensive picture of this specific innovation environment. A mixed-methods, explorative approach was used: a literature analysis, followed by an expert workshop and semi-structured expert interviews, was conducted to understand the barriers for development and implementation of such innovations. A SWOT workshop assisted in generalizing results from selected innovation examples. A complementary two-wave Delphi study was used to identify innovation activity, important actors, policies and drivers within horticulture. Based on these data, we were able to identify different barrier-types, showing how they are interconnected and affect innovation processes increasing ecological modernization of the sector.