Junta leader Assimi Goita signed the code into law on Monday, his office announced on social media Tuesday.
The mining code reform could boost the national budget by 500 billion CFA francs ($820 million), economy minister Alousseni Sanou said this month.
The new mines minister, Amadou Keita, said the state hoped the mining industry would eventually contribute to between 15 and 20% of GDP.
According to analysts, the reform allows the government to hold up to 10 percent equity in new projects with the option to buy an additional 20% during the first two years of commercial production. And it allows the Malian private sector to hold up to five percent.
The new code also removes tax exemptions for mining companies during operations.
Mali, a poor Sahel country, is one of Africa's leading gold producers.
It is also boasts manganese and lithium — two minerals key to the global energy transition — though these have not been extensively explored.
Mali produced 72.2 tonnes of gold in 2022, including six tonnes by artisanal gold panners, then-mines minister, Lamine Seydou Traore, said in March.
Gold accounts for 25% of the national budget, 75% of export earnings and 10 percent of GDP, he added.
Mali's mining sector is dominated by foreign companies, including the Canadian firms Barrick Gold and B2Gold, Australia's Resolute Mining and the British Hummingbird Resources.
They have continued to operate despite political instability and an expanding jihadist insurgency.
"Mali's demand for higher stakes in mining projects ... reflects a wider trend across the continent where resource-rich countries, impacted by the knock-on effects of global shocks, aim to increase their control over the mining sector," Mucahid Durmaz, an analyst with Verisk Maplecroft, said.
But, he added, the Malian government is "walking a tightrope" and must be "cautious not to scare away investors."