Harambee Stars' hopes of playing in a second successive Africa Cup of Nations tournament were dashed after going down 2-1 away to Comoros on Sunday night.
The hosts got their goals through El Fardou Ben and Faiz Mattoir, while Cliff Nyakeya scored Stars' consolation.
In the second match of a doubleheader against the Islanders, Kenya enjoyed much of the possession throughout the match but fell behind after just 21minutes through Ben's goal.
Mulee's men kept knocking on Comoros' goal and their hard work paid off as Nyakeya drew them level in the 34th minute to ensure it was all square going into the break.
The hosts, however, regained their lead five minutes into the second half as Mattoir finished a superb team move, and it proved the winning goal.
Stars threw everything at their hosts in the last minutes of the match, but solid defending and good goalkeeping from Salim Ben Boina proved tough to break.
Coach Jacob Ghost Mulee made a number of changes, recalling Lawrence Juma and David 'Calabar' Owino, who failed to make the starting lineup during Wednesday night's match at the Moi Kasarani Stadium.
The rest of the team remained largely unchanged, with Arnold Origi starting in goal, while Victor Wanyama captained the side, taking his spot in midfield alongside Johanna Omollo and Eric Johanna.
Cliff Nayakeya and Ayub Timbe were tasked with troubling Comoros' defence through the wings.
What next for Stars?
Stars will now have to beat Egypt and Togo in the remaining two matches to qualify for the continent's biggest football tournament.
Meanwhile, Comoros have one foot in next year's tournament as they lead the standings on eight points, two ahead of Egypt, who play away to Togo on Tuesday night.
Harambee Stars Starting Team: Arnold Origi, David Odhiambo, Eric Ouma, Joseph Okumu, Brian Mandela, Victor Wanyama, Johanna Omollo, Lawrence Juma, Ayub Timbe, Cliff Nyakeya, Masoud Juma.