[1][3] After some time in private legal practice,[3] Batohi entered public service in 1986 as a junior prosecutor at the magistrate's court in Chatsworth, Natal.

[6][7] Later in 2000, she was appointed to replace Chris MacAdam as the head of the KwaZulu-Natal branch of the Scorpions, an elite investigative unit of the National Prosecuting Authority.

[13] In the aftermath of the interviews, Radebe's advisory panel announced a final shortlist of five nominees which included Batohi, as well as Siyabulela Mapoma, Simphiwe Mlotshwa, Rodney de Kock, and Andrea Johnson.

[15] Commentators noted that her decade at the Hague meant that she was relatively well-insulated from the NPA's internal politics,[9] while the Democratic Alliance's Glynnis Breytenbach said she was "a very good administrator".

[32] However, in December 2021, Cronje announced her resignation from the unit,[33] sparking rumours that she was frustrated by the NPA's lack of capacity and even had clashed with Batohi as a result.

[36][37] Alongside her focus on corruption, Batohi announced the revival of NPA investigations into the apartheid-era crimes traversed at the Truth and Reconciliation Commission.

[38] A contingent of NPA prosecutors and Hawks investigators were seconded to a unit dealing exclusively with over 100 such matters,[39][40] and Batohi asked the judiciary to reopen inquests into the deaths of anti-apartheid activists Neil Aggett and Hoosen Haffajee.

[38] In June 2022, she said that the Justice Minister, Ronald Lamola, was likely to establish an inquiry to investigate whether the prosecution of apartheid-era crimes had been obstructed by political interference under past governments.