The Bloc Quebecois won 10 seats in Monday's election, but failed to capture a key one - its leader's seat.
NDP incumbent Helene Laverdiere re-captured the Laurier-Sainte Marie riding that she took from Duceppe in 2011.
Duceppe resigned as head of the party and left politics after losing in the last election, but returned to the party's helm earlier this year in an apparent bid to bolster the Bloc's numbers.
The Bloc had two seats at dissolution, and only one of those people kept his seat: Louis Plamondon, the longest-serving MP in Canada.
Claude Patry, who was elected as an NDP representative in 2011 but switched parties, lost his riding.
The Bloc Quebecois now has 10 seats, but a political party must have at least 12 Members in the House of Commons to be a recognized party.
Meanwhile the Bloc's support as a percentage of the popular vote dropped, from 6.04 percent in 2011, to 4.7 percent in 2015.
In his speech at the end of the night, Duceppe said the party fell short of its objective but came a long way.
He also said he believes it is better to be a country in the world than a province in Canada.
Duceppe did not resign as the party's leader, and said on Tuesday afternoon that a decision about his leadership would be made later in the week.
"We will have a meeting on Thursday among the elected MPs, and we will make a decision as to what happens in the future," he said.
After Duceppe stepped down as leader in 2011, party members chose Mario Beaulieu as leader, who in turn stepped down as leader earlier this year because of a poor showing in polls.
Beaulieu ended up winning the only Bloc seat on the island of Montreal, with 18,535 votes, compared to 15,740 for the Liberal candidate and 14,698 for the NDP.
When asked if the separatist movement was dying, Duceppe was less than enthusiastic.
"It's obvious we have a lot of work to do [to attract youth], but I don't think there is a lot of popular support for federalism either," said Duceppe.
"Does it mean we have to end our task? I don't think so."
He said the separatist movement does have to work hard to fight the assimilation of francophones.
"When we look elsewhere, I met people with the Scottish National Party, in Catalonia, in recent years and they thought their movements were dead. But we see there has been a resurgence."