Ocean acidification, characterized by a gradual seawater pH decline, influences marine primary producers such as diatoms, which contribute substantially to oceanic carbon fixation. Experimental studies aiming to project climate change impacts often simulate acidification via abrupt pH shifts, potentially misrepresenting ecological and evolutionary responses. Here we conducted a long-term evolution experiment with the marine diatom Chaetoceros muelleri, comparing abrupt and gradual CO₂ increases from 440 to 1000 ppm over 1100 generations. Integrating evolutionary genomics, physiological assays, elemental stoichiometry, and Earth System Modeling, we found that abrupt acidification exaggerated diatom growth and carbon fixation responses by up to 15%, driven by enhanced divergent genomic signals and persistent gene expression changes. Gradual acidification elicited weaker phenotypic and genomic shifts, aligning more closely with natural ocean conditions. These findings suggest that models based on abrupt CO₂ increases may overestimate the contribution of Chaetoceros muelleri and maybe also other diatoms to productivity and biogeochemical cycling under ocean acidification, highlighting the importance of gradual pH decline in experimental designs to accurately predict marine ecosystem responses.