The founders Frank Muether, Micki Wentzel und Stefan Wentzel developed a concept for a private school for the education of children in Kenya. Mekaela Academies is registered as an educational organisation and purchases its first plot. Beginning of construction of the first primary school which is named "Manuel Alexander School" (MAS) to honour the first donor. The construction of the first building is completed in 1996, it has three classroom for approx. 90 pupils, an office and a teachers' room.

Several classrooms are added to MAS. Due to riots in the area many families living in South Coasts flee their homes into their tribal territories. At the peak of the crisis, the number of pupils drops from 200 to 90, the project faces termination. Donations from Germany help rescue the project. A sports field, a playground and a third building are built.

Construction of a second primary school, called "Likunda Primary School" (LPS) as a boarding school. Two school buildings a dining hall and some provisional dormitories are erected.

Introduction of computer lessons as subjects without exams at Mekaela Academies. The boarding section of LPS is extended, around 400 pupils are attending MAS and LPS which are operating at their maximum capacity. The planning for a third school, Lulu High School (LHS), commences. At LHS, the graduates of the two primary schools MAS und LPS may attend their secondary level.

Construction and completion of Lulu High School, the first secondary school of Mekaela Academies, with capacities for up to 200 students. Due to increasing demand for places in the primary section, LPS implements a second stream. Beginning of a cooperation with the German foundation "Eine-Welt-Stiftung" to build "Heshima Primary School" (HPS) as the third primary school of Mekaela Academies. Establishment of a school newspaper "Mekaela Times" run by pupils and teachers.

Completion of the first building of HPS with three classrooms. MAS and LPS achieve a position among the top 20 of about 18,000 primary schools (Source: HSK) in Kenya during the 2007 KCPE exams. The first KCSE exams are conducted at LHS in 2007, Mekaela Academies has "produced" its first university students. About 95% of the 2007 graduates of LHS qualify for university, and LHS achieves a position among the top 100 secondary schools among approx. 3,000 Secondary Schools.

Mekaela Heshima Primary School receives boarding facilities. Capacity at Lulu High School is extended from 200 to 300 pupils. Mekaela Academies operates two school farms with acreage of approx. 30 (12 ha) to sustain supply of basic foodstuff (maize, vegetables, milk) to the schools. Likunda Primary School and Lulu High School receive the donation of a solar power generation equipment from Phoenix Solar AG in Germany to provide independent power supply.

Introduction of internet to all schools, connecting computer classes and providing free internet access for teachers and pupils. Free basic medical coverage provided to all children through an integrated medical scheme (MMMS) through co-operation with local doctors and hospitals. Organising and conducting FANYA famine relief missions to the drought-stricken province Turkana in the North on Kenya with exclusively voluntary helpers recruited among the teachers and the parents of pupils of Mekaela Academies. Implementation of an employment agency (Noble Domestic Agency) for unemployed parents of students of Mekaela Academies.

Lulu High School (LHS) as well as parts of neighboring Likunda Primary School (LPS) being destroyed by a fire on Valentine's Day 2013. The damage amounts to around 30 million Kenya shillings (300,000 Euros) of which less than half is covered by insurance. A fund-raising campaign in Europe raises approx. 150,000 Euros and enables re-constructions of both schools by the end of 2013. Several terror attacks (December 2013) and the outbreak of Ebola in Africa (mid 2014) lead to a collapse of the tourism industry of Kenya's South Coast by more than 50%. Inevitably, hundreds of parents of Mekaela Academies pupils lose their jobs. In October 2014, Mekaela Ratinga Junior School joins Mekaela Academies as fifth school with a new concept. School fees at Ratinga are less than half of those of its sister schools in order to make education more affordable for children of families with very low incomes.

In April 2015, Manuel Alexander School and adjacent Mekaela Heshima Primary School are destroyed by a fire, only two dormitories remain intact. The damages amount to nearly 28 million Kenya Shillings (250,000 Euros) of which only around 40% are covered by insurance. The balance was raised through donations. The reconstruction of MAS and MHS is completed in September 2015. All schools of Mekaela Academies replace their Makuti roofs with metal roofs. In October 2015 the donor-funded expansion of Mekaela Ratinga Junior School to a full primary school school is completed and the term "Junior" is dropped from the name of the school.