Macroalgae are critical components of coral reef ecosystems. Yet, they compete for space with corals, and in case of environmental disturbances, they are increasingly involved in phase-shifts from coral-dominated to macroalgae-dominated reefs. As regard to climate change, ocean acidification (OA) has been shown to be detrimental to corals and could favor macroalgal proliferations. However, little is known about the effects of OA on macroalgal phenotypes. Comparative metabolomic studies are particularly relevant to assess phenotypic responses of macroalgae to stress as some seaweed are known to produce a large diversity of specialized metabolites involved in various ecological functions. The main aim of our study was to explore the impact of OA on the metabolome of brown macroalgae using Lobophora rosacea as a model species. This species is widespread in New Caledonian lagoons where it is a key component of coral-algal interactions. Metabolomic changes were analyzed using Liquid Chromatography-Mass Spectrometry (UPLC-HRMS) applied to three different OA scenarii: low and variable pH over a long-term timescale (in situ at Bouraké), low and constant pH over a short-term timescale (ex situ experiment), and current pH (control). Different metabotypes were defined in diverse pH conditions, and a significant decrease in some specialized metabolites concentrations was noticed at low pH including lobophorenols B and C as well as other oxylipin derivatives. We suggest a down-regulation of metabolic pathways involving lobophorenols, in low pH conditions, or their transformation, which is in accordance with the optimal defense theory. In addition, we used Microtox ® bioassays as a proxy for macroalgal toxicity and found no significant differences between low pH and control samples. This study details the first metabolomic-based study on a fleshy macroalgae in response to OA and provides new insights for this important functional group producing a large number of metabolites in response to their close environment.