Cymru Premier clubs Airbus UK Broughton and Cefn Druids have won their appeals for Football Association of Wales (FAW) Tier One licences for 2020-21.
Newtown were also successful in their appeal to be granted a Uefa licence.
Second-placed Cymru North side Flint Town United also appealed successfully.
But Cymru North promotion leaders Prestatyn Town, along with Swansea University, failed to overturn the FAW decision and are ineligible to compete in the JD Cymru Premier next season.
That means Prestatyn will be unable to compete in the JD Cymru Premier next season even if they win promotion, assuming the season is completed once the coronavirus crisis has passed.
A Prestatyn statement read: "The club are disappointed not to have been granted our Tier One licence on appeal at today's FAW panel meeting.
"We are waiting on the official letter from the FAW to explain why the clubs appeal was not successful and then the board will discuss the next steps."
The FAW Tier One Licence is required for clubs to participate in the Cymru Premier.
For those clubs who qualify for European competitions, a Uefa licence is also a pre-requisite.
In addition, the independent appeals body also ruled in favour of Aberystwyth Town, Caldicot Town and Cardiff City Women for Tier One licences to compete in the Welsh Premier Women's League next season.
Cardiff City Women also made a successful appeal to have a Uefa licence granted.
All unsuccessful clubs had 10 days in which to submit a challenge and the independent appeals body met remotely on Wednesday, 29 April, to give its decisions.
The FAW has suspended domestic football at all levels in Wales until at least 15 May due to coronavirus and has said "every possible option" is being looked at to conclude the season.
Originally the FAW had suspended domestic football until 4 April, and then again until 15 April.