Last week, the interior minister offered to resign after rejecting the deal Merkel made at EU summit in Brussels.
Merkel and Seehofer have been embroiled in a dispute for weeks over the minister’s plan to start turning away migrants - who have already registered elsewhere in the EU - at the German border.
If Seehofer withdraws his support for Merkel, she would be left without majority support in the German parliament, and this might lead to early elections.
While the two are at loggerheads, on-the-ground organisations like Über den Tellerrand and the Muslim Women’s Centre for Encounter and Further Education help migrants to feel right at home.
At Über den Tellerrand the integration of migrants, and building of communities, is done through cooking. Über den Tellerrand means "beyond your plate", and was started in 2013 in Berlin as a student project but has since developed into a means to integrate recent migrants into Germany.
Noor Edres, one of the co- ordinators at Über den Teller- rand, said the project was aimed not only at integrating migrants into German society, but showing Germans that they can all live together as neighbours.
All of this is done through cooking classes and lessons. Über den Tellerrand organises cooking events where locals and migrants meet and get to know each other through sharing their food and culture.
The events have so far produced three cookbooks, and there are satellite offices in over 30 places across Germany, Europe and the US.
Edres said: “We realised how easy it is to bring people together through cooking and eating. Cooking together ensures that encounters are at eye level so everyone's the same, it doesn't matter the language - and this removes pressure from people.
"Many of the people who came here had nothing, they had lost everything, so being able to share a part of their culture makes them proud. Somehow, with food, you can open up encounters.” Through the cooking classes, migrants also get to learn German and meet locals who might be able to help them find jobs."
In Cologne, nearly 600km away, the Muslim Women's Centre for Encounter and Further Education is also trying to assist mostly women and children to integrate into German society.
The organisation was founded in 1996 and currently employs mostly women from 40 different countries. Though called the Muslim Women’s Centre for Encounter and Further Education, it assists women from all religious backgrounds.
Since 2000, the organisation has helped more than 400 women from 80 countries, including Bulgaria, Pakistan, Lebanon, Japan and India, complete their high school education. Besides this, the centre assists women with learning German, refugee counselling, migration advisory services, childcare services and donations for clothes.
One of the employees, Sabira Bouhired, said the aim was to offer women education and empower them.
“We have a few clients who are men, because the demand is high now. This is mainly because more than half the migrants from the Arab world are men. But women are still our priority,” Bouhired said.
She admits that, because of growing hostility against Muslims across Europe, the last five years have not been easy. But it is all about building partnerships.
“People who are connected with Muslims see no problem with them. In some areas, it is still harder to get a job with a hijab or a Muslim-sounding name,” she said.
To help change perspectives, the organisation invites police officers and schoolteachers to meet and talk to some of their members.
Edres echoes this belief, saying that all people want is to be treated with humanity.
“Of course when you don't know the other side it’s easy to create your idea of who this person is. Once you meet the people, you can change your mind. Every single person is unique, and has past experiences, and we need to take that into account. People are so sick of having their identity as that of a refugee. One guy asked: 'When am I going to graduate from being a refugee. It has been three years?' ”