A critical review and analysis of the literature relevant to the phenolic content of eucaryotic microalgae was performed. Several issues were identified and discussed. In summary, the main problems with the reporting on the phenolic content of microalgae are the following: (1) despite its usefulness in the determination of phenolic content in plant samples, the Folin–Ciocalteu assay is non-suitable for microalgal research due to the high presence of interfering compounds in microalgal extracts such as chlorophyll and its derivatives in organic extracts and free aromatic amino acids or nucleotides in aqueous extracts; (2) while there is chromatographic evidence for the presence of simple phenolic acids in most microalgal clades, the lack of critical enzymes of phenolic biosynthesis in most microalgae, as well as the high variability of phenolic profiles even in the same genus, require more extensive research before conclusions are drawn; (3) the accumulation and metabolism of external phenolics by microalgae has been almost universally neglected in studies focusing on the phenolic content of microalgae, even when natural seawater or complex organic media are used in the cultivation process. Despite these issues, the literature focusing on the bioremediation of waste streams rich in phenolics through microalgae demonstrates the ability of those organisms to adsorb, internalize, and in many cases oxidize or transform a wide range of phenolic compounds, even at very high concentrations. Simple phenolics found in waste streams, such as olive mill waste, have been shown to enhance the antioxidant activity and various bioactivities of microalgal extracts, while complex biotransformation products of phenolics have also been characterized. In conclusion, the de novo biosynthesis of phenolic compounds via eucaryotic microalgae requires further investigation with better designed experiments and suitable analytical methods, while the response of microalgae to phenolic compounds in their growth medium is of great practical interest, both in terms of waste treatment and for the production of functional foods, cosmetics, and pharmaceuticals.