Maclura tinctoria is a tree species native from Brazil and rich in phenolic compounds. Since plant antibacterial activity is highly associated with phenolic compound concentration, we aim to evaluate the in vitro antimicrobial activity of different extracts against fish pathogenic bacteria. In addition, some phenolic compounds have central depressant effects and can be useful in aquaculture due to possible sedative and/or anesthetic effects. Four M. tinctoria extracts were extracted separately with ethanol; leaves (LE), bark (BE), heartwood (HE), and the sapwood (SE). In vitro antimicrobial activity was tested against Aeromonas strains at concentrations of 6400 to 3.125 μg/mL. The sedative effect was evaluated for 24 h with 30 and 100 mg/L concentrations. Chemical composition was analyzed by HPLC-DAD-MS. The HE extract had the best MIC (400 µg/mL) and MBC (800 µg/mL) compared to the LE, BE, and SE extracts. LE extract induced deep sedation and the BE, SE, and HE extracts induced light sedation. Additionally, BE, SE, and HE induced a normal behavior without side effects. Polyphenolic compounds with antimicrobial activity and sedative effects were identified mainly in HE. Thus, HE extract is safe and can be used as a sedative for silver catfish.