WASHINGTON (TNND) — The longest shutdown in U.S. history is over, but Congress is now facing another funding deadline with most of its full-year spending bills needing approval and a continuing battle over expiring health care subsidies that were at the center of the six-week standoff.

The bipartisan deal to end the shutdown funds the government through January and only included long-term agreements on just three of the 12 bills Congress needs to pass each year to keep agencies running and programs funded, creating another deadline for lawmakers to find bipartisan compromises. Full-year legislation has only been approved for tame issues like funding for veteran affairs, food aid, programs for farmers and Congress itself.

That leaves most of the discretionary U.S. budget left to be negotiated over the coming weeks, with the government still operating on funding levels set last year when former President Joe Biden was still in office. President Donald Trump and congressional Republicans have sought to reduce government spending since his return to office and could look to make more contentious cuts in the full-year bills.

Among the departments still needing full funding packages are Homeland Security, State and Treasury, all of which have been at the center of heated debates over the Trump administration’s policy and the White House’s attempt to take authority over congressionally allocated spending.

"When you knock out the easy appropriations bills early, all you're doing is delaying the conflicts, you're not resolving them," said Matthew Green, a political science professor at Catholic University.

Democrats have already signaled there may be issues coming to compromises with Republicans on the remaining spending bills that include the most divisive issues facing appropriators.

“There are nine bills to go,” said Rep. Rosa DeLauro, the top Democrat on the House Appropriations Committee. “The bills that have come forward have been nothing but unilaterally partisan bills. So those will have to be negotiated.”

But Democrats are also motivated to get full-year spending bills in place to avoid more moves from the White House to shift, freeze or cancel billions in congressionally approved funds.

“Passing full-year funding bills to ensure that Congress — not Trump or Russ Vought —decides how taxpayer dollars are spent. We should never turn the keys over to Trump and his cabinet secretaries, allowing them to make unilateral cuts and to shift funding around however they please,” Sen. Patty Murray, the top Democrat on the Appropriations Committee, said in a floor speech this week.

House Republicans have said they are committed to passing each of the individual 12 spending bills rather than in a massive omnibus that has become more common in recent years. They said reopening the government would allow for appropriations talks to move forward.

“I look forward to continuing the fiscal year 2026 appropriations process in the coming weeks. And I hope that, having seen the consequences of this historic shutdown on the American people, it is not a political stunt repeated in the future,” Rep. Tom Cole, the top House appropriator, said during a Rules Committee hearing.

In the Senate, Majority Leader John Thune said after the stopgap was passed that the Senate would get to work on advancing more funding measures once they return to session early next week. A handful of spending bills will be up for consideration in a package including funding for defense, labor, transportation and housing.

Adding to the potential stumbling blocks is what will happen to the soon-to-be-expiring Affordable Care Act subsidies that were Democrats' sole demand in the shutdown impasse. Thune has promised Democrats a vote next month on extending them, but their passage is far from certain, and House Speaker Mike Johnson has shown no interest in holding a similar vote. Some House Democrats have suggested there could be another shutdown if no progress is made in negotiations to keep the subsidies going or finding another solution, but it's unclear whether the senators who broke ranks with the party to reopen the government would be willing to have another.

Many Democrats were enraged at the eight senators who agreed to reopen the government with Republicans and are certain to keep the expiring subsidies as a central issue moving forward. Some Republicans want to sunset the enhanced subsidies that were passed during the pandemic and are considering other alternatives, though others have expressed interest in negotiating an extension that includes income caps and other restrictions to who has access to them.

The issue is likely to linger into next year's midterm elections, which could also influence lawmakers' interest in another shutdown as campaign season heats up.

"It's not an accident that the Senate Democrats who voted for the CR to end the shutdown, none of them are running in 2026. The midterms might make some Democrats even more scared of losing a primary, and they might say, 'we really have to shut the government down now, My base is screaming about it,'" Green said. "On the other hand, by then, maybe Democrats have decided the way they win is by focusing on inflation, focusing on the Epstein files, things that aren't directly related to appropriations."