Tropical coral reefs provide important ecosystem goods and services that are supported by one or more ecosystem functions (e.g., recruitment, primary production, calcification, and nutrient recycling). Scleractinian corals drive most of these functions, but a combination of global and local anthropogenic stressors has caused persistent shifts from coral- to algae-dominated benthic reef communities globally. Such phase shifts likely have major consequences for ecosystem functions; yet, related knowledge is scarce in general, but particularly at the community level, under ‘in situ’ conditions, and under the influence of changing environmental variables. Thus, we conducted a series of interconnected in situ experiments in coral- and algae-dominated reef communities in the central Red Sea, combining traditional community ecology approaches with novel metabolic and biogeochemical assessments from December 2016 to January 2018. Specifically, we (i) examined the influence of coral-algal phase shifts on recruitment and succession patterns, (ii) assessed the role of benthic pioneer communities in reef carbon and nitrogen dynamics, (iii) developed a novel approach to measure functions of structurally complex reef communities in situ, and (iv) quantified biogeochemical functions of mature coral- and algae-dominated reef communities. The findings suggest that coral-algal phase shifts fundamentally modify critical reef functions at different levels of biological organization, namely from pioneer to mature reef communities. For example, community shifts, through a lower habitat complexity and grazing pressure, decreased the number of coral recruits by >50 %, thereby inhibiting the replenishment of adult coral populations. At the same time, a 30 % higher productivity (annual mean) and increased organic carbon retention in algae-dominated communities supported a fast biomass accumulation and community growth, altering the habitat-specific community metabolism and reef biogeochemistry. Seasonal warming amplified these functional differences between coral- and algae-dominated communities, likely promoting a positive feedback loop of reef degradation under predicted ocean warming. Overall, this dissertation provides quantitative data on critical functions of classical and phase shifted novel reef communities, on tipping points for the collapse of community functions, and potential future winners and losers. The knowledge gained with this thesis helps, thereby, to understand how phase-shifted reef ecosystems function and which services will be generated in comparison to coral-dominated reefs under near-future stress scenarios.