The kippa protest follows last week's assault on two young men wearing the skullcaps.
Head of the Central Council of Jews in Germany Josef Schuster warned people in Germany not to wear yarmulkes in major cities following a series of anti-Semitic attacks.
The head of the main Jewish umbrella in Germany has recommended that Jews not wear kippahs in public in its major cities.
Thousands of Germans wearing Jewish caps took part in nationwide rallies on Wednesday evening in support of the Jewish community amid concerns about growing anti-Semitism. About the same number are non-practising Jews or people with Jewish roots in Germany.
"Defiantly showing your colours would in principle be the right way to go", he told German public radio.
She told Israel's Channel 10 TV network that aside from anti-Semitism by right-wing groups, similar threats were coming from some Muslim refugees in the country. "Nevertheless, I would actually advise people against openly wearing a kippah in metropolitan Germany".
Mr Schuster's comments apparently contradict the position taken on the kippah issue by the Berlin-based Jewish Forum for Democracy and Against Anti-Semitism - the organisation which shared video of last week's attack on Facebook.
German Chancellor Angela Merkel, who has encouraged the mass migration of Muslim refugees to Germany, recently suggested that the current wave of anti-Jewish sentiment could be called the "new anti-Semitism" and might be blamed in part on some of those Muslim refugees.
"We sounded warnings very early about the huge strength of Muslim anti-Semitism", said senior AfD member Georg Pazderski.
"I used to always advise my Jewish friends and acquaintances not to wear a kippah so as not to show their Jewish identity".
"On no account do we want this music prize to be a platform for anti-Semitism, contempt for women, homophobia or for belittling violence", it said in a statement. "I changed my opinion", a spokesman said.
Since 1991, the number of Jews belonging to a religious community has more than tripled to more than 100,000, boosted by an influx from the former Soviet Union.