The proliferation of cyanobacteria and, consequently, the production of cyanotoxins is a serious public health concern; for their control, several alternatives have been proposed, including physical, chemical, and biological methods. In the search for new alternatives and a greater understanding of the biochemical process involved in the blooms’ formation, we report here the effect of eight phenyl-acyl compounds in the growth of Microcystis aeruginosa Kützing (assesed as cell density/count and Chl a fluorescence concentration) morphology, and production of the toxin microcystin-LR (MC-LR). Caffeic acid and eugenol decreased the growth of M. aeruginosa Kützing and the levels of Chl a. However, 3,5-dimethoxybenzoic acid and syringic acid caused the opposite effect in the growth; 2′and 4′only affected the Chl a. A reduction in the concentration of the MC-LR toxin was detected after treatment with syringic acid, caffeic acid, and eugenol. According to HPLC/MS (High Performance Liquid Chromatography coupled to Mass Spectrometry), a redox process possibly occurs between caffeic acid and MC-LR. The optical microscopy and Scanning Electron Microscopy analyses revealed morphological changes that had been exposed to caffeic acid and vanillin, specifically in the cell division and presence of mucilage. Finally, assays in Daphnia pulex De Geer neonates indicated that caffeic acid had a non-toxic effect at concentrations as high as 100 mg/L at 48 h.