Harebottle will run Cape Town-based Kropz SA from March.
It is unlisted but 26%-owned by African Rainbow Capital Investments (SJ:AIL).
Harebottle left Gemfields after it was taken over by former major shareholder Pallinghurst Resources (SJ:PGL) in mid-2017.
Kropz said in August its Elandsfontein phosphate project in South Africa had been delayed because of water licensing problems, "technical issues identified during commissioning" and a 10-year low in phosphate prices.
Kropz director Mike Nunn, who worked with Harebottle at Tanzanite One, said it was a great hire for the company.
"I have been lucky enough to have worked with Ian for many of his 17 years in mining and have experienced first-hand his positive, professional and thorough approach to business leadership," he said.
"Ian has a built an enviable reputation as being a positive ‘disruptor' and one to challenge traditional practices."
Harebottle framed the company as part of the global push to feed people in a tougher climate.
"In my lifetime, we have seen exponential population growth coupled with a commensurate decrease in available arable land, which makes the role of increasing crop yields incredibly relevant both today and in the future," he said.
"I have been extremely impressed with the way in which Kropz has established itself in setting high standards for the sustainable mining of plant nutrient minerals and believe Kropz is the ideal platform to build the leading sub-Saharan plant nutrient producer and trader."