We report results of a deep all-sky search for periodic gravitational waves from isolated neutron stars in data from the first Advanced LIGO observing run. This search investigates the low frequency range of Advanced LIGO data, between 20 and 100 Hz, much of which was not explored in initial LIGO. The search was made possible by the computing power provided by the volunteers of the Einstein@Home project. We find no significant signal candidate and set the most stringent upper limits to date on the amplitude of gravitational wave signals from the target population, corresponding to a sensitivity depth of 48.7 [1/Hz−−−√]. At the frequency of best strain sensitivity, near 100 Hz, we set 90% confidence upper limits of 1.8×10−25. At the low end of our frequency range, 20 Hz, we achieve upper limits of 3.9×10−24. At 55 Hz we can exclude sources with ellipticities greater than 10−5 within 100 pc of Earth with fiducial value of the principal moment of inertia of 1038kg m2.