Ms Jacobs took up the chief executive role with the council in February 2018, replacing Leanne Mash.
Last March, elected members unanimously agreed to reappoint Ms Jacobs in the role, extending her appointment to 2025.
Speaking to the Otago Daily Times, Ms Jacobs said it had been an "absolute privilege"to work with the council and she had mixed feelings about leaving the role.
Her tenure with the CODC had been "one of the most challenging and rewarding jobs" of her career.
The council had some big achievements — the release of the nationally recognised destination management plan; a growing relationship with iwi; becoming a living wage council within existing budgets; the traction made with the Eden Hore collection, which is "a taonga for our district", and the gains made in raising Central Otago’s profile nationally through her and Central Otago Mayor Tim Cadogan’s roles on the boards of Taituarā and Local Government New Zealand respectively.
But it was the small things that had the biggest impact, she said.
"I guess it comes down to getting positive outcomes for our people ... It comes down to relationships and honouring them," she said.
"The big shiny things are really great but it’s the little things and building trust that matters ..."
Reform had been an overarching feature of the last three years and it was a challenging time for councils, she said.
"Reforms have opportunities and most are worthwhile doing but for CODC to operate in this environment is challenging.
"Members of the public can think that council is a faceless entity when there are humans that get up and go to work each day."
The region had a stable council and people should not take that for granted, she said.
"It was a dream job — I always wanted to live in Central Otago and the Central Otago District Council was my ticket to that."
Mr Tim Cadogan said Ms Jacobs had been an "exceptional leader" of the management side of council and he was saddened to accept her resignation.
Ms Jacobs had given three months’ notice with a final end date to be agreed.
She will be taking up the position of director local government with engineering consultancy Beca, and performing her new role from Alexandra.
