The 66-year-old made the announcement during Sunday's morning mass at the catholic St. Martin's ministry in the Upper-Bavarian town of Zorneding, where he had been shepherd to the congregation since 2012.
During the final months of 2015, the priest was racially insulted by a local politician and then received five anonymous death threats, the Süddeutsche Zeitung reports.
Police are now looking for the people who sent the letters, who are being investigated on three charges including incitement of racial hatred.
In a statement issued by the archdiocese of Munich on Monday, Ndjimbi-Tshiende said the situation had been a burden on him and that he felt relief once he had made the decision to step down.
Though he doesn't feel resentment towards the community, he is looking forward to taking on a new role within the Catholic church and to being able to focus on his service to God, the statement said.
Sign of the town Zorneding in Upper Bavaria; Photo DPA
"[It's] terrible, very terrible", said town mayor Piet Mayr of the Christian Social Union (CSU).
"I hope that they [the death threats] are not coming from Zorneding locals" but from "psychopaths from the outside." according to the Sueddeutsche Zeitung (SZ).
'Live up to your Christian duty!'
Hostilities between Ndjimbi-Tshiende and sections of the local community appear to go back to November 2015 when then-CSU local chairman Sylvia Boher wrote an article for the party's local publication claiming the state of Bavaria was overrun by refugees.
The CSU are a conservative political party who dominate Bavarian politics and whose leader has strongly resisted Germany's open-door refugee policy.
In the article Boher described the refugee influx as an "invasion" and accused Eritrean asylum seekers of trying to run away from their military service.
Ndjimbi-Tshiende reacted angrily top the letter, calling on politicians to live up to their Christian duty.
Deputy CSU chairman Johann Haindl shot back at the priest in an article in the Ebersberger Zeitung, referring to him as "unser Neger" – a historically derogatory term for black people in Germany, comparable to the word "Negro".
The two politicians faced harsh criticism for their comments, forcing both to resign from their roles in the party, but Sylvia Boher remained still active in the local council.
Ever since then, tensions in the community of Zorneding have been bubbling and seething.
Deputy mayor Bianka Poschenrieder of the centre-left Social Democratic Party (SPD) recalled to the SZ an instance when a townsperson told her that the priest wasn't going to be with the community for a very long time.
"It sounded a lot like a threat," she said.
Only later did it come out that the priest had been receiving death threats for months.
A heated debate has broken out as to what extent the CSU is responsible for the priest stepping down.
"What happened in Zorneding is a disgrace for Germany and the CSU/CDU. Shame on them," one Twitter user commented.
Was in #Zorneding passiert ist, ist eine Schande für Deutschland und die CSU/CDU. TRAURIG!!- Arbeiterkind (@MasterExtin) March 7, 2016
"What does the 'C' of CSU stand for again?"; asked another Twitter-user.
But Mayor Mayr said that the CSU "is in no way responsible for people who act outside of the boundaries of the law."
The provisional chairwoman of the CSU Zorneding, Jutta Sirotek, said she stands behind tolerance and human dignity and condemns any kind of racism.
This isn't the first ugly incident of threatening behaviour to have affected the town.
In November of 2014 the head of a local primary school offered a vacant room in her apartment to a group of under-age, unaccompanied refugees, leading to her being bombarded with xenophobic e-mails.
But some of the community want Ndjimbi-Tshiende to stay and have launched a petition called "Unser Pfarrer muss in Zornedingen bleiben!" (Our priest must stay in Zorneding!).