In 2006, Ahern ran for sheriff unopposed, replacing Charles Plummer who resigned after five terms in office.
In response Ahern vowed to change department policy so that deputies activate their body cameras at all times.
[8] Two deputies were charged by the San Francisco District Attorney's office with felonies including assault by a public officer, battery with serious bodily injury, assault with a deadly weapon and several enhancements for great bodily injury and use of a weapon.
[10] Ahern came under criticism about conditions at the Santa Rita Jail, where at least 68 inmates died between 2011 and 2020, largely from suicides and overdoses.
[13] A US Department of Justice report released April 2021 found that the jail had become the county's largest provider of mental health services, and that its inadequate provision of care of inmates constituted a violation of their civil rights.
[14][15] In February 2022, a federal judge approved a settlement calling for improved mental health services and staffing, to the objections of some inmates and advocacy groups.