In March 2013, Mutua was sworn in as the first governor of
Machakos County, which is one of the 47 counties established under the Constitution of Kenya. He was elected on a
Wiper Democratic Movement Party ticket alongside
Bernard Kiala as his deputy governor. In August 2016, Mutua launched a political party called
Maendeleo Chap Chap Party. This was a culmination of several months of speculation among the Kenyan media and general public that Mutua had abandoned
Wiper Democratic Movement – the party that had sponsored him for his election as Machakos Governor in 2013. Mutua's action of launching and supporting a political party other than the one that sponsored him was considered controversial. He was expected to vacate office and seek a fresh mandate as
Machakos County Governor; being sponsored by his new political party in line with Kenyan electoral laws. When Mutua did not vacate office to seek fresh re-election,
Wiper Democratic Movement Party's disciplinary committee found him culpable of launching and supporting another political party. The disciplinary committee deemed him to have resigned from the party. In November 2016, a notice to impeach Mutua was filed in the Machakos County Assembly by a member Mr. Stephen Muthuka. This was after the motion notice was signed by 46 out of 59 Machakos county assembly members – meeting the two-thirds threshold for an impeachment motion to progress. Included among the reasons for the impeachment motion was alleged breach of the Kenyan constitution, procurement laws and
devolution laws. Several days before Mutua's impeachment motion at the Machakos County Assembly, over half of the assembly's 59 members travelled out of the country in what was considered to be a tactical move for scuttling the impeachment process. In the absence of 32 members of the county assembly, the impeachment motion was debated with Mutua being represented by his lawyer. When the final vote was taken 26 out of 27 members of the assembly voted to impeach Mutua. This, however, was too few votes to legally impeach Mutua as Governor of
Machakos County since the threshold of 40 members of the county assembly voting in favor of the motion was not attained.
2017 gubernatorial election Mutua contested the Machakos County Governor position for a second and final term in the
2017 general election against
Wavinya Ndeti and his former Deputy –
Bernard Kiala. Mutua was declared the winner amid claims of election rigging which resulted in a protracted election petition process that saw high court judge Aggrey Muchelule annul Mutua's election. In June 2018, The court of appeal bench comprising judges W. Ouko, M. Warsame and S. Gatembu Kairu nullified the election of Alfred Mutua. Subsequently, Alfred Mutua contested the ruling of the Court of Appeal at the Supreme Court. This legal contest was considered an epic battle at the Kenyan apex court. The Supreme Court of Kenya would later on 21 December 2018, overturn the Court of Appeal ruling to reinstate Mutua's gubernatorial election win.
Stewardship of public funds Though Mutua's stewardship of public funds as Governor for
Machakos County saw the Auditor General raise numerous queries on the propriety of public expenditure throughout his first term, it turned out that his strategy of fiscal management was one of the best in the government. For example, in 2014, he chose to purchase second hand vans and retrofitted them into ambulances which enabled him to have 120 ambulances at the cost of a few new ones. This got him into trouble with the Auditor General, but was a big win for Machakos residents who got at least one ambulance in every location. In the years 2015, 2019 and 2020, Mutua was ranked the best-performing governor in Kenya. In 2015, a survey carried out to measure the successes of county government in satisfying their constituents also ranked Mutua's Machakos the best. ==Gubernatorial tenure performance==