Enzyme-assisted aqueous extraction (EAAE) is a green, and scalable method to produce oil and protein hydrolysates from fish. This study investigated the role of different parameters on emulsion formation, oil recovery, and the composition of crude oil during EAAE of Baltic herring (Clupea harengus membras). Fatty acid compositions, lipid classes, tocopherols, and oxidation status of the EAAE crude oils were studied. Compared to solvent-extracted oil, EAAE resulted in a lower content of phospholipids accompanied by a 57% decrease in docosahexaenoic acid. Changing fish to water ratio from 1:1 to 2:1 (w/w) with ethanol addition led to the greatest reduction (72%) of emulsion, which resulted in an increase in oil recovery by 11%. The addition of ethanol alone, or reduction of enzyme concentration from 0.4% to 0.1% also reduced emulsion-formation significantly. Overall, emulsion reduction resulted in higher content of triacylglycerols and n − 3 polyunsaturated fatty acids in the crude oil extracted.