The troubles have come thick and fast since the five-year-old Alternative for Germany reached a key goal in October by entering the last of the country's 16 state assemblies, winning 13 percent in the region of Hesse.
A relative newcomer feared and loathed by the bigger mainstream parties, the AfD has however now stagnated at around 15 percent in the polls while another party, the left-leaning Greens, has booked a series of stunning successes.
Billing themselves as “the alternative to the Alternative” with a clear stance against the AfD's anti-immigration message, the Greens are now polling at around 20 percent, making them the second-strongest party after Merkel's CDU-CSU bloc.
The AfD meanwhile have faced charges of accepting illegal campaign funds from a non-EU donor, in Switzerland — an especially damaging charge for a party that accuses all the “establishment parties” of being dishonest and corrupt.
Co-leader Alice Weidel has been under fire after media reports said her party chapter received 130,000 euros from a Swiss entrepreneur.
While she has rejected wrong-doing and said the money was returned, German
prosecutors in mid-November asked parliament to lift Weidel's immunity as they stepped up their enquiries.
A more fundamental, long-term problem may be that the AfD's declared nemesis, Merkel, has rung in the beginning of the end of her chancellorship after 13 years in power.
Weakened by several election setbacks for her CDU, she has declined to stand again for the leadership of the party at a December congress and declared she will leave politics when her term ends in 2021.
The AfD, whose main slogan has been “Merkel must go”, may hail the news as a triumph as they have long railed against Merkel over her decision to allow more than one million asylum seekers into the country since 2015.
But they may yet come to miss the leader on whom they have projected their discontent, typically by portraying Merkel wearing a Muslim headscarf or with bloody vampire fangs on protest posters and in social media posts.
“When Merkel goes, the AfD will need a new object of hate,” wrote the Berlin daily Tagesspiegel.
“With her retreat, Angela Merkel may have achieved something in which she previously failed: to truly hurt the AfD.”
Much will depend on who succeeds Merkel at the helm of the party.
If Merkel's preferred successor, the moderate Annegret Kramp-Karrenbauer, nicknamed “mini-Merkel”, wins the race, the AfD will likely be happy to train their sights on her.
The other two candidates — corporate banker Friedrich Merz and right-wing Health Minister Jens Spahn — may however be tougher targets since they have signalled shifting the party back to the right, including on immigration.
In this case, “the AfD will probably lose some of its voters,” said Sudha David-Wilp, a researcher at think-tank the German Marshall Fund.
The AfD itself is still deeply divided between relative moderates who joined the party when it started as a mainly eurosceptic group, and its openly revisionist and far-right members.
Its most extreme major figure, Björn Höcke, has demanded “a 180-degree shift” in the nation's culture of remembrance and atonement over Nazi crimes and the Holocaust — an era which another leader, Alexander Gauland, has termed a “speck of bird shit” in Germany's long history.
This summer the AfD, which was long labelled “right-wing populist”, for the first time publicly closed ranks on the streets with the anti-Islam Pegida movement at mass rallies in the eastern city of Chemnitz where neo-Nazis performed Hitler salutes.
The country's domestic intelligence services have started surveillance of some members of the AfD's youth wing, JA, for links to right-wing extremists — a fate the AfD as a whole wants to avoid at all cost.
Last week the party executive declared that it had noted “with disgust” statements made by some members of the JA organisation that betrayed a “contempt for humanity”, and demanded they be excluded from the group.
The same week a leading member, Steffen Königer from Brandenburg state, left the AfD, declaring that in many regions “the moderates within the AfD have lost the battle against the destructive ones once and for all”.