At Wednesday's meeting, Morales offered the new government investment in the co-operatives and the promise to expand where the groups can mine.
The miners ended the protests and headed home on Wednesday night.
The negotiations revealed the delicate relationship between Morales and Bolivia's estimated 60,000 independent miners, who backed his 2005 election but have since been in dispute with his administration over access to the country's increasingly valuable mineral deposits.
Rising international metal prices, fed in part by demand from China, have doubled the value of Bolivia's mineral exports, from $547m in 2005 to more than $1bn last year, with co-operatives accounting for just over a third.
The metals - mostly zinc, silver, gold, and tin - represent Bolivia's largest export after natural gas.
But the Bolivian government only collected $45.5m in mining taxes in 2006, with co-operatives paying $18.6m.
Morales seeks to dramatically increase the government's collections this year, perhaps to as much as $300m.
The proposed tax increase is a first step toward Morales' announced goal of nationalising Bolivia's mining sector, a process that critics say remains vague beyond proposed tax increases.