The extract of microalga Nitzschia laevis (NLE) is considered a source of dietary fucoxanthin, a carotenoid possessing a variety of health benefits. In the present study, the bioaccessibility and deacetylation of fucoxanthin were studied by simulated in vitro gastrointestinal digestion and colonic batch fermentation. In the gastric phase, higher fucoxanthin loss was observed at pH 3 compared to pH 4 and 5. Lipases are crucial for the deacetylation of fucoxanthin into fucoxanthinol. Fucoxanthinol production decreased significantly in the order: pure fucoxanthin (25.3%) > NLE (21.3%) > fucoxanthin-containing emulsion (11.74%). More than 32.7% of fucoxanthin and fucoxanthinol was bioaccessible after gastrointestinal digestion of NLE. During colon fermentation of NLE, a higher loss of fucoxanthin and changes of short-chain fatty acid production were observed but no fucoxanthinol was detected. Altogether, we provided novel insights on the fucoxanthin fate along the human digestion tract and showed the potential of NLE as a promising source of fucoxanthin.