1992–1997 Kenyan Parliament

Kenya's first multiparty elections were held in 1992. Musyoka stayed in KANU, renewed his parliamentary position and was appointed as the Minister for Foreign Affairs and International Cooperation. He also held couple of other ministerial positions while part of the KANU government. In June 1993, he addressed the World Conference on Human Rights in Austria which was the first human rights conference held since the end of the Cold War. He termed the illicit mineral trade which fuels and finances what he called 'the cause of incessant conflicts, environmental degradation but ultimately and sadly too, poverty'.^[9] The Vienna Declaration and Programme of Action was the major result from this meeting after the participants reached a consensus.^[10]

1997–2002 Kenyan Parliament

He was again elected to the parliament at the 1997 elections, but now from Mwingi North Constituency, since his former constituency Kitui North was split into new constituencies.^[11]

2002–2007 Kenyan Parliament

In the months leading up to the 2002 general election, under the leadership of then KANU secretary general, Raila Odinga, he decamped from KANU to join the Liberal Democratic Party (LDP) as a founding member under the banner of the National Rainbow Coalition, which went on to win the general elections.

On 1 December 2003, as the Minister for home affairs and international co-operation for Kenya, he welcomed the people to this meeting, whose theme was Strengthening the role of IGAD in regional peace initiatives and post conflict reconstruction on behalf of the republic of Kenya and thanked the Danish government, IGAD Secretariat and the ISS on behalf of the^[12] IGAD Member States for their preparations and funding of the meeting. Kalonzo Musyoka was involved in the Sudan peace process between 1993 and 1997 and he was part of the team that reconstituted the draft establishing IGAD in 1995.

Musyoka became Minister for Foreign Affairs for a second time under President Mwai Kibaki, but in a cabinet reshuffle on 30 June 2004 he was moved to the post of Minister for Environment. In late August 2004, he was additionally removed from his position as chairman of the Sudanese and Somali peace talks and was replaced by John Koech.^[13] Musyoka was reportedly unhappy with President Kibaki's refusal to honour a pre-election Memorandum of understanding (MOU) which they had signed with the president's party NAK. He was one of the leaders of the successful "No"-campaign in the November 2005 referendum on the proposed new constitution. Following the referendum, he was dismissed from the Cabinet.^[14]

Subsequently, Kalonzo Musyoka decamped Liberal Democratic Party (LDP) into the little-known Labor Party of Kenya.^[15]

Kalonzo Musyoka was widely expected to vie for the presidency in the December 2007 election. Musyoka campaigned for the ODM-Kenya ticket, facing a number of other contenders. His rating for December 2007 election steadily dropped, and political analysts wondered whether he would make a significant impact. His relationship with fellow ODM-Kenya leader Raila Odinga, who was also after the ODM-Kenya presidential ticket, was the subject of much speculation. Many observers questioned whether the presidential hopefuls of ODM-Kenya, particularly Raila and Musyoka, could unite to support one common candidate for the general election.

The ODM-Kenya split into two factions, one gathered around Musyoka and the other around Odinga, in August 2007. Musyoka was elected by his faction as its presidential candidate on 31 August 2007,^[16][17] receiving 2,835 votes in a secret ballot against Julia Ojiambo, who received 791 votes.^[17]

Musyoka has been quoted as saying "... the war against poverty could not be won unless environmental issues were addressed."^[18]

Musyoka launched his presidential campaign at Uhuru Park in Nairobi on 14 October 2007. This move was criticised by those who saw him as a traitor to the ODM party of Raila Odinga. December 2007 polls put Odinga ahead and Kibaki following closely, Kalonzo however said that "atapitia katikati" (passing between two people).

After 2007

According to official results, Musyoka placed a distant third behind Kibaki and Odinga with 9% of the vote.^[19] Amid a violent crisis over the results, with supporters of Odinga disputing the outcome, Kibaki appointed Musyoka as vice-president and Minister of Home Affairs on 8 January 2008.^[20] Musyoka expressed gratitude to Kibaki and, referring to the ongoing dispute and violence, said that he was "intensely aware that the appointment has come at a difficult time when our nation is going through a painful moment".^[14] He took office as vice-president on 9 January.^[21]

The political crisis eventually led to the signing of a power-sharing agreement between Kibaki and Odinga. In the Grand Coalition Cabinet that was announced on 13 April 2008, Musyoka remained vice-president and Minister of Home Affairs.^[22][23]

In 2010 Musyoka supported the draft constitution in the campaign for 4 August referendum but Members of the campaign team opposing the draft constitution claimed that he was secretly opposing the draft leading to a satirical comparison of Musyoka to a watermelon which is naturally green outside and red inside, the team supporting the draft constitution was represented by color green while the team opposing the draft constitution was represented by the color red hence the "green team" and the "red team", Musyoka's nickname watermelon was because of his alleged open support for the green team and secret support for the red team.^[24] Most of the opposition of the draft constitution were the clergy.

2013 Elections

In the race for the 4th president of Kenya, Kalonzo Musyoka joined his longtime political opponent Raila Odinga to form the Coalition for Reforms and Democracy (CORD) with Musyoka shelving his presidential ambition to run as Odinga's running mate.^[25][26]

When the first round of the presidential election took place on 4 March 2013, Uhuru Kenyatta was declared the president-elect of Kenya by the Independent Electoral and Boundaries Commission. Raila Odinga challenged this in the Supreme Court of Kenya. Questions were raised why Musyoka was not a petitioner in the case.

After the Supreme Court dismissed the CORD Petition, he left office when the President-elect, Uhuru Kenyatta, was sworn in.

2017 Elections

For the 2017 general election, Musyoka once again joined Raila Odinga to form the National Super Alliance to oppose president Kenyatta and deputy president William Ruto.^[27] Musyoka then ran under Odinga as his running mate.^[28]

2022 Elections

In the 2022 elections, Musyoka announced that he would vie for presidency; he however dropped his presidential bid and supported Azimio la Umoja candidate Raila Odinga.^[29]