Muyoti replaced Ugandan tactician Paul Nkata, who left the club after the match-fixing claims by club chairman Cleophas Shimanyula.
Muyoti joined Homeboyz alongside Peter Okidi, formerly of Nakuru All-Stars, who will be the new assistant coach.
"It is a new challenge for me once again and with the demands that come with the job at Kakamega Homeboyz, I want to make sure that we achieve the targets the club had set before the season kicked off.
"My expectations here are still the same as I will strive to do everything possible and get the best result before the end of first leg. I also want to thank Nzoia Sugar for the chance they gave me to handle the side and I wish them a good season," Muyoti told Goal.
Muyoti and Okidi joined Homeboyz on a one year contract each. The rest of the technical bench will remain the same.
Striker Allan Wanga was elevated to the position of the head coach in an acting capacity, following Nkata’s exit early in February.
Apart from Nzoia Sugar, Muyoti has also handled AFC Leopards.