Trinamool Congress leader Mukul Sangma lost from Tikrikilla and along with him, his wife Dikkanchi D Shira and brother Zenith Sangma also lost in the Assembly elections on March 2.
However, he is leading in Songsak 41 constituency.
During the initial hours, Sangma was leading in both seats in Meghalaya, however, soon after that the figures changed and he faced defeat.
While casting his vote on February 27, Sangma had said that the people of Meghalaya were fed up with the corruption and misgovernance of the ruling National People's Party.
''They want change, and I am confident that TMC will emerge as the alternative," he added.
The elections in Meghalaya are being closely watched by political analysts, as they are expected to have a bearing on the national political landscape. The results of the elections will be announced on March 2, and it remains to be seen which party will come out on top.