At an EU summit, von der Leyen proposed a so-called ETS investment booster aimed at promoting investment in clean technologies.
The money would be financed through the sale of ETS certificates, she said after the meeting in Brussels.
According to von der Leyen, EU member states with lower incomes in particular should have access to the money.
Under the ETS, businesses in some sectors, including in electricity generation, must buy allowances for their greenhouse-gas emissions.
Parts of industry have criticised the system, citing rising production costs that make it harder to compete with companies outside the EU.
The summit did not yield any tangible results in the dispute over the future of the ETS.
Countries such as Poland continue to call for easing measures, while others, including Spain, insisted on maintaining the current approach.
Germany has recently advocated for limited adjustments, for example regarding how many free certificates industrial plants should receive.
A planned review of the system by the European Commission by the end of July is intended to help stabilise the CO2 price and mitigate its impact on electricity prices, according to a joint statement by EU leaders.
The CO2 price is subject to fluctuations, particularly in times of crisis, as it is largely determined by supply and demand.
