Mutant received widespread acclaim from contemporary music critics. At Metacritic, which assigns a normalized rating out of 100 to reviews from mainstream critics, the album received an average score of 81, based on 21 reviews, which indicates "universal acclaim".
Mark Richardson of Pitchfork gave the album a very positive review, stating, "Compared to Xen, Mutant feels less composed and less indebted to classical music. With many tracks on the former album you could squint a little bit and imagine them being performed by a daring new music ensemble, à la Aphex Twin with Alarm Will Sound. But Mutant leans toward soundscape, avoiding proper songs." Richardson concludes, "On Mutant, Ghersi turns a fixation on porousness and instability into a kind of spiritual pursuit."
Writing for Exclaim!, Daryl Keating said Mutant "is an album that is eventually rewarding, but only to those who are determined to follow its scattered pathway to the satisfying, aggregate end."