Abstract Fishery by-products can be better utilized following enzymatic hydrolysis treatment to produce fish protein hydrolysates (FPH) with potentially enhanced interface-stabilizing properties (e.g. functionality). The production of FPH could be accelerated through the application of rapid heating methods [e.g. microwave-assisted heating (MW)] rather than slower conventional heating (CH) treatments. The objective of this study was to investigate the effects of microwave heating during enzymatic hydrolysis on the functionality and antioxidant properties of FPH. Trout by-products were hydrolyzed with Alcalase at an enzyme substrate ratio (E:S) of 0.5, 1.7, and 3.0% (w/v), respectively, for 3, 5 and 15 min using a microwave system (1200 W, 20% power with 50% duty cycle at 50–55 °C) and a conventional heating method (water bath at 50 °C). The degree of hydrolysis and protein solubility was higher ( P < 0.05) for the MW-FPH than for the CH-FPH. MW-FPH at 5 min (0.5% E:S) demonstrated higher ( P < 0.05) emulsifying activity and emulsion stability than CH-FPH with the same treatment. Foam capacity and stability were also greater ( P < 0.05) for MW-FPH samples that were treated 15 min by microwave-assisted heating (0.5% E:S) when compared to CH. Overall, MW-FPH exhibited higher ( P < 0.05) 2,2-diphenyl-1-picryhydrazyl and ferric ion reducing capacity than CH-FPH. We therefore conclude that microwave-assisted hydrolysis is an alternative method to produce FPH with improved solubility, emulsifying activity, foaming properties and antioxidant activity.