Despite his many successes, during the last twenty years of his life Alexios lost much of his popularity. This was largely due to the harsh measures he was forced to take in order to save the embattled empire. Conscription was introduced, causing resentment among the peasantry, despite the pressing need for new recruits to the imperial army.

In order to restore the imperial treasury, Alexios took measures to tax the aristocracy heavily; he also cancelled many of the exemptions from taxation that the church had previously enjoyed. In order to ensure that all taxes were paid in full, and to halt the cycle of debasement and inflation, he completely reformed the coinage, issuing a new gold hyperpyron (highly refined) coin for the purpose. By 1109, he had managed to restore order by working out a proper rate of exchange for the whole coinage. His new hyperpyron would be the standard Byzantine coin for the next two hundred years.

The final years of Alexios's reign were marked by persecution of the followers of the Paulician and Bogomil heresies—one of his last acts was to burn at the stake the Bogomil leader, Basil the Physician; by renewed struggles with the Turks (1110–1117).