Roy, 64, died on Sunday following a multiple organ failure while undergoing treatment at the Medanta hospital in Gurugram.
A 21-gun salute was accorded to Roy, who was President of United Democratic Party (UDP), a key partner in the National People's Party-led Meghalaya Democratic Alliance government.
Roy's body, draped in the tricolour, was brought to the Sohra stadium from his Saitsohpen residence on a flower bedecked carriage, escorted by Meghalaya Police personnel amid the inclement weather.
Various political leaders, including Chief Minister Conrad Sangma and his cabinet colleagues, Leader of Opposition Mukul Manda Sangma, Deputy Speaker Timothy Shira, and former Speaker Bindo Mathew Lanong recalled Roy's contribution to the state.
"Apart from all the positions that he (Roy) held, the qualities he had and all work he did, I think, above all, Dr. Donkupar Roy was a good human being. We will all remember him as a good human being," the Chief Minister said.
Recalling his long association with Roy, Mukul Sangma said: "Roy was a leader who put the interest of state before everything and his commitment to join politics showed his interest to served the people."
Speaking on behalf of the bereaved family, Roy's eldest son Balajied Kupar Synrem, expressed his gratitude for the public support during their moment of loss.
Braving the inclement weather, people in large numbers assembled at the stadium to catch a last glimpse of their leader and bid him a tearful adieu.
They also participated in his last journey from Sohra to Jatap.
Roy was first elected to the Meghalaya Assembly from Shella constituency, bordering Bangladesh, as an Independent MLA on 1988 with the ardent support of the then Alliance Reconstruction of Meghalaya State, a political body of the influential Khasi Students' Union.
He was first appointed as Minister in the B.B. Lyngdoh ministry and then served in various capacities in the state.
After a fractured mandate in the 2008 Assembly elections, Roy was sworn in as Chief Minister on March 19, 2018 but his government was dismissed exactly one year later and the state put under President's Rule.
( With inputs from IANS )