President Uhuru Kenyatta's indictments by the International Criminal Court (ICC) strained his relationship with civil society.
Although the frosty relations began before the 2013 General Election, they got worse just after the President and his deputy William Ruto were sworn in for their first term.
Uhuru and Ruto had contested the presidency on a joint ticket despite having been indicted by ICC over their alleged role in the 2007-2008 post-election violence, a development various civil society leaders opposed.
Civil society, through various campaigns and strategies, worked round the clock to facilitate justice for the victims of poll violence.
When Mwai Kibaki's administration showed little signs of taking action against the perpetrators of the violence, civil society led calls for the matter to be referred to the ICC.
The agencies became more vocal in demanding that Kenya cooperates fully and fulfils its international legal obligation to The Hague-based court under the Rome Statute. The calls for justice for victims grew even louder as the two individuals spent much of their first term in office fighting off the charges at the ICC.
Eventually, the court dropped the charges against Uhuru in December 2014, and the prosecution (then under Gambian national Fatou Bensouda) accused the Kenyan authorities of blocking the case by not cooperating with investigators.
It was at this point that the Jubilee administration set upon the civil society over its role and decided to make life difficult for several NGOs.
"During Uhuru's reign, the civil society was largely apprehensive and suspicious, as the Jubilee administration closed the space, turned hostile, particularly to the human rights discourse," says Joseph Omondi, the executive director at the Midriff Hurinet, a human rights organisation.
Mr Omondi recalls that at one point, the government accused them of promoting foreign interests. Because of this, the Jubilee government moved to control NGOs. Loyal MPs escalated the anti-NGOs campaign. But it was in 2016 that the government began to clamp down on civil society through the NGO Coordination Board.
The board threatened to deregister 959 NGOs over alleged misappropriation and embezzlement of donor funds, diversion of funds, undeclared foreign funding, money laundering and terrorism financing.