In Lent 1496 he proclaimed the duty of resisting the pope when in error.

In November a new brief proposed changes in the constitution of his order which would bring him more directly under the power of Rome.
Savonarola replied that he did not fear the excommunication of the sinful church, which, when launched against him May 12, 1497, only made him more defiant.

Claiming to be commissioned directly from God, he appealed to the powers to summon a general council against the pope.
At this juncture one of his opponents, a Franciscan, Francis da Puglia, proposed to him the ordeal by fire, stating that though he expected to be burnt he was willing to take the risk for the sake of the faith.
The challenge refused by Savonarola was taken up by his friend Fra Domenico da Peseta, and although forbidden by Alexander, the ordeal was sanctioned by the Signory and a day set.

A dispute as to whether Domenico should be allowed to take the host or the crucifix into the flames prevented the experiment from taking place, and the mob, furious at the loss of its promised spectacle, refused further support to the discredited leader.

For some years, members of his own order, who resented the severity of his reform, had cherished a grievance against him, and now they had their chance.