Glyphosate is the main active component of the commercial formulation Roundup®, the most widely used chemical herbicide worldwide. However, its potential high toxicity to the environment and throughout trophic webs has come under increasing scrutiny. The present study aims to investigate the application of bio-optical techniques and their correlation to physiological and biochemical processes, including primary productivity, oxidative stress, energy balance, and alterations in pigment and lipid composition in Phaeodactylum tricornutum, a representative species of marine diatoms, using the case study of its response to the herbicide glyphosate-based Roundup® formulation, at environmentally relevant concentrations. Cultures were exposed to the herbicide formulation representing effective glyphosate concentrations of 0, 10, 50, 100, 250, and 500 μg L−1. Results showed that high concentrations decreased cell density; furthermore, the inhibition of photosynthetic activity was not only caused by the impairment of electron transport in the thylakoids, but also by a decrease of antioxidant capacity and increased lipid peroxidation. Nevertheless, concentrations of one of the plastidial marker fatty acids had a positive correlation with the highest concentration as well as an increase in total protein. Cell energy allocation also increased with concentration, relative to control and the lowest concentration, although culture growth was inhibited. Pigment composition and fatty acid profiles proved to be efficient biomarkers for the highest glyphosate-based herbicide concentrations, while bio-optical data separated controls from intermediate concentrations and high concentrations.