Makwatta who had been loaned out to AFC Leopards by Kenya Police FC from January till the end of the season penned a two-year deal.
Gaborone United has also signed Kenya Police FC forward and midfielder Duncan Otieno for a two-year deal.
“I made the decision to leave because of the current situation back at home. Things were not looking okay in terms of football administration and as a player, you always look to where there is stability and Gaborone also offered a chance to play in the CAF Champions League,” Makwatta told a local media outlet.
Makwatta joined the Patrick Aussems side early this year after a poor season show at Kenya Police FC.
His form at Ingwe attracted several suitors and at the end, made the decision to move to Botswana.