The soursop fruit or Annona muricata (A. muricata) fruit is recognized by its bioactive compounds and acetogenins (ACG) are among the most important. The effect of ACGs, with greater importance in health, is that they present anti-tumor activity; however, the methods of extraction of ACGs are very slow and with a high expenditure of solvents. To our knowledge, there is no report of an optimal method for the extraction of acetogenins from the Annonaceae family by ultrasound-assisted extraction (UAE); therefore, the aim was to find the best UEA conditions of acetogenins from A. muricata fruit (peel, pulp, seed, and columella) by using response surface methodology. The effect of amplitude (40%, 70%, and 100%), time (5, 10, and 15 min), and pulse-cycle (0.4, 0.7, and 1 s) of ultrasound at 24 kHz was evaluated on the total acetogenin content (TAC). Optimal extraction conditions of acetogenins (ACGs) with UEA were compared with the extraction of ACGs by maceration. The optimal UEA conditions in the A. muricata pulp and by-products were dependent on each raw material. The highest TAC was found in the seed (13.01 mg/g dry weight (DW)), followed by the peel (1.69 mg/g DW), the pulp (1.67 mg/g DW), and columella (1.52 mg/g DW). The experimental TAC correlated well with the model (Adjusted R2 with values between 0.88 and 0.97). The highest effectiveness in ACG extraction was obtained in seeds and peels using UEA compared to extraction by maceration (993% and 650%, respectively). The results showed that A. muricata by-products are an important source of ACGs and that UAE could be a viable alternative, with high potential for large-scale extraction.