Several regulars, including veteran captain Emilio Nsue, have also been removed from their squad for their last Group H qualifier against Liberia on Monday, officials said on Sunday.
Key players refused to travel for their penultimate group qualifier last Thursday, citing continual complaints over conditions and money, after which the coach and some players were kicked out of the squad.
Micha's dismissal was confirmed in a social media post from the Equatorial Guinea Football Federation.
"The Ministry of Sports has given players called up for these FIFA matches who believe they can continue to defend their country the opportunity to put their names on a list," the statement added.
"Otherwise, anyone who doesn't do so will be deemed to have opted out and will no longer be part of the national team."
A new squad has since been named for Monday's match, with Casto Nopo appointed interim coach.
The list excludes many of the players who were in the squad at the last Cup of Nations, where Equatorial Guinea caused a major sensation by beating hosts Ivory Coast 4-0 in the group phase.
The result was hailed as the biggest shock in Cup of Nations history and followed a surprise 1-1 draw with Nigeria in their opening fixture of the tournament in early 2024.
Equatorial Guinea finished ahead of the two heavyweights in the group standings but were then eliminated in the last 16 by a last-gasp goal for Guinea.
Since then, Equatorial Guinea have qualified for the upcoming Cup of Nations finals in Morocco, which kicks off on December 21, but are out of contention for a place at next year’s World Cup.