The coup was ostensibly carried out to restore order and prevent further attacks on Anjouanese residents in Grande Comore amid the country's secession crisis involving the islands of Anjouan and Mohéli.

During his short-lived reign, the country adopted a new constitution that limited the local autonomy of the islands and strengthened the use of Islamic law, fueling unrest and helping spark the secession crisis.

[1] By April 1999, the Organization of African Unity (OAU) brokered a reunification accord that would grant greater autonomy to Anjouan and Mohéli and introduce a rotating presidency.

[3] On April 29, 1999,[4] amidst the turmoil engulfing Grande Comore, the Comorian military, led by Colonel Azali Assoumani, staged a bloodless two-day long coup and ousted President Massonde to stop the escalating violence.

[4] By 2000, amid growing international criticism of Azali's regime, he promised to relinquish power by April 14 of that year, under the condition that Anjouan rejoined the republic.