While in Indonesia, the Chinese minority there were slightly marginalized in the national movement because of ethnic differences. Resulting in a number of nationalist political parties finding it difficult to accept them. This resulted in the Communist Party (PKI) attracting a number of Chinese who were disillusioned by nationalist parties who would not accept them as members, and who were attracted by its radical and non-racial approach.[4]
While in the Netherlands, apart from establishing the Indonesian Chinese Peranakan Union, Tan was also a member of the Dutch Communist Party (Communistische Partij Nederland, CPN) which was influenced by Paul de Groot. Tan Ling Djie was not the only Chinese left, but there were still Oei Gie Hwat, Tjoa Sik Ien, and Siauw Giok Tjhan.[3]
When the Madiun Affair broke out, Tan Ling Djie was arrested while attending the Railway Workers Union Conference (SBKA) in Yogyakarta. For three months, he had to languish in prison. Meanwhile his roaming friends like Amir and Musso had to end their lives at the hands of government soldiers. The sudden attack by the Dutch army against the capital city of Yogyakarta in the Second Dutch Military Aggression on 19 December 1948 allowed political prisoners imprisoned in Yogyakarta to escape, including Tan Ling Djie. They were also no longer being hunted by government soldiers who were busy dealing with the Dutch military.
Following the disastrous Madiun Affair, Tan Ling Djie was named as one of the leaders of the illegal PKI along with Amir Sjariffudin, Maruto Darusman, Abdulmadjid, Setiadjit, and Wikana. They took over the leadership of the PKI from Alimin and Sardjono. He also became secretary general of the Preparatory Committee for the Fusion of 3 Parties, namely the PKI, the Indonesian Labor Party, and the Socialist Party.[5] Tan Ling Djie was arrested and held without charge for a time as part of the August 1951 mass arrests.
Meanwhile, D. N. Aidit in a paper entitled About Tan Ling Djie-ism which was presented at the 5th National Congress of the Indonesian Communist Party in 1954, which was later published in the Red Star, mentions Tan Ling Djie, "as Secretary General of the Socialist Party concurrently as a leading member of the 'illegal PKI' Politburo, then since August 1948 as Deputy Secretary General of the PKI. "[6]