Dozens of chanting activists went to the Anglo-Dutch firm's base in The Hague, where they delivered a legal summons with a court date set for April 17.
"This is a unique case," Roger Cox, lawyer for Dutch climate group Milieudefensie, told AFP
"We are taking Shell to court because it's not keeping to the aims of the Paris climate agreements. This way we are trying to prevent huge damage."
The environmental groups say some 17,200 people have registered as co-complainants in the case, which Cox said would be the first of its kind.
Other groups involved in the case include ActionAid Netherlands, Both Ends, Fossielvrij NL, Greenpeace NL and Young Friends of the Earth NL.
In a summary of the 250-page document handed over to Shell, the groups said that under Dutch law Shell was unlawfully endangering peoples' lives by not acting to prevent global warming.
"Internal and external documents show that Shell has known about climate change at least since the 1950s and has been aware of its large-scale and serious consequences at least since 1986," it said.
"Although Shell knew, it has not taken any serious steps to minimise its share in climate change," the document added.
- 'Expose Shell' -
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Cox said that unlike previous cases which sought financial compensation for the effects of climate change, this one involves asking the judge to order Shell to ensure its activities have zero percent carbon dioxide emissions by 2050.
Shell is responsible for 1.7 percent of all greenhouse gas emissions between 1988-2015, according to a peer-reviewed study of the 100 most polluting companies released two years ago.
It is also among five oil and gas majors that have spent more than $1 billion on lobbying against climate legislation since the Paris deal.
Shell's plans for tackling climate change are "not consistent with the Paris goals", said Harjeet Singh, who heads up global climate activities at ActionAid.
"We need to expose Shell on this and in fact what it has been doing all this while is hiding and distorting facts and lobbying against climate policy," Singh told AFP.
Climate change is a pressing issue in the Netherlands, where at least a third of the country lies below sea level.
The Dutch government was ordered by a court last year to slash greenhouse gases by at least 25 percent by 2020, following a legal challenge by another environmental group.
Thousands of Dutch students have rallied in Amsterdam and The Hague in recent weeks, urging the government to take action, with Dutch Prime Minister Mark Rutte meeting the group's leaders.