All three organisations were shut down in Turkey following the July 15 coup attempt last summer.
The United Nations Economic and Social Council (ECOSOC), one of the six major UN agencies, cancelled on Wednesday at Turkey's request the consultative status of three groups linked to Fetullah Gulen's organisation.
US-based Gulen is accused by Ankara of masterminding the July 15, 2016 failed coup in Turkey. Ankara uses the acronym FETO (Fetullah Terrorist Organisation) to refer to Gulen's operation.
ECOSOC came to a consensus after voting to terminate all affiliation with the Kimse Yok Mu Relief Foundation, the Journalists and Writers Foundation (JWF), and the Turkish Confederation of Businessmen and Industrialists (TUSKON).
"The decision was made unanimously… It was the outcome of Turkey's initiative," Turkey's Foreign Minister Mevlut Cavusoglu was quoted as saying by Anadolu Agency.
All three organisations were shut down in Turkey following the July 15 coup attempt last summer, in which more than 200 died and over 2,000 were injured.
Consultative status gives non-governmental organisations various rights of access and engagement, including UN passes, the right to be represented at designated meetings and to have their documents translated and circulated as official UN documents.
According to the Turkish government, Kimse Yok Mu - on paper an NGO focused on humanitarian aid - was transferring donations collected to FETO.
The government alleges that the primary goal of the Istanbul-based Journalist and Writers Foundation was to recruit writers and journalists to further Gulen's agenda and spread misinformation.
The government determined that the third group, the Turkish Confederation of Businessmen and Industrialists, was also linked to Gulen, and involved in extortion and money laundering.
The 54-member ECOSOC also cancelled the consultative status applications for two other Gulen organisation-linked groups.
Turkey's Permanent Mission to the UN praised the move as "an important success" in the fight against FETO at international agencies.