The lawsuits came on the heels of a lawsuit filed on Wednesday challenging other recent moves to undo Obama's climate change regulations.
The move would mark the beginning of a process that could be lengthy. Approvals are needed from state regulators, and the project could face legal challenges.
The protest follows months of demonstrations in a remote part of North Dakota, where the Standing Rock Sioux tribe demonstrated in an attempt to stop the Dakota Access Pipeline.
Greenpeace argued in its letter that Exxon Mobil would "directly and predictably" benefit from the approval of Keystone XL because the firm has investments in Canadian oil sands.
Protesters were set to gather in a number of U.S. cities on Wednesday, a day after the U.S. Army said in a legal filing it planned to cancel an environmental study and grant the final easement needed to complete the Dakota pipeline.
Protesters have rallied for months against plans to route the Dakota Access pipeline under a lake near the Standing Rock Sioux reservation, saying it threatened water resources and sacred Native American sites.
While oil producers in Canada and North Dakota are expected to benefit from a quicker route for crude oil to U.S. Gulf Coast refiners, a revival of the projects would mark a bitter defeat for Native American tribes and climate activists.
"The pipeline would not make a meaningful long-term contribution to our economy," the president said.
The controversial project now awaits an administration decision on whether to permit or deny it.
The temporary injunction was prompted by a lawsuit from 70 landowners who don't want the pipeline on their property.
A final decision from the President could come as early as February.
The Nebraska Supreme Court's decision reversed a lower court that had blocked the proposal and cleared the way for a U.S. State Department ruling on the plan.
President's former press secretary hints that Obama may veto the pipeline.
In a 59 to 41 vote, the U.S. Senate narrowly voted to reject the Keystone XL pipeline Tuesday evening after several hours of intense debate.
The leader of the First Nation says he will close the reservation's borders to prevent installation of the pipeline
The Senate was still one vote shy of the 60 needed to overcome a filibuster, or blocking procedure, and pass a companion bill, an aide to a Keystone supporter in that chamber said.
Obama cited pending legal action in Nebraska and said it was hard to evaluate the pipeline proposal until the actual route was known.
Meanwhile, Canada has been heavily mining the Alberta region for tar sands for several years. The consequences are piling up.
The spill occurred in a popular spot for shorebirds, just before the migratory season is set to begin
After temporary construction jobs, the pipeline's employment impact will be minuscule, the report says