After working in several organizations, his government career started when he was elected into and became deputy speaker of the People's Representative Council (DPR) in 1999 until 2009.

[5] During the anniversary of Gus Dur's death in 2016, Iskandar described in an editorial on Tempo magazine about his father who buried an abangan Muslim, illustrating him as an example of humane behavior.

[7] Iskandar completed his middle school equivalent in a state-funded madrasa in his hometown (Madrasah Tsanawiyah Negeri Jombang), graduating in 1982.

His thesis was titled Perilaku Kapitalis Masyarakat Santri: Telaah Sosiologi tentang Etos Kerja Masyarakat Desa di Jawa Timur (Capitalistic Behavior of Santri: Sociological Study on East Java's Rural Population Work Ethic), and he graduated with a bachelor's degree in 1992.

[9] His thesis was titled Manajemen Hubungan Masyarakat Partai Kebangkitan Bangsa dalam Pemilu 1999 (Public Relations Management of the National Awakening Party in the 1999 Election).

[1][9] He was also member of Komite Nasional Pemuda Indonesia (Indonesian Youths' National Committee) in which he served as vice president of the Yogyakarta branch.

After concluding his studies he moved to Jakarta and worked at the Institute for Islamic and Social Studies as a secretary, Lembaga Pendapat Umum (Public Opinion Institute, founded by Gus Dur) as the research division head, and became active in ForumDemokrasi which was a harsh critic of then-president Suharto.

[1] After the fall of Suharto, the new party participated in the 1999 election and won 12.6% of the national votes, securing 51 seats in the People's Representative Council and becoming the third-largest group behind PDI-P and Golkar.

[1][9] PKB's coalition in the People's Consultative Assembly would then deliver Abdurrahman Wahid to become the 4th President of Indonesia in a vote The Economist described as "a shock", defeating Megawati Soekarnoputri 373 against 313.

[16] Later on, after being reelected for his second term in the 2004 election, he would continue serving in his post after he was re-elected along with other coalition politicians, with Agung Laksono as speaker.

[17] He stated in an interview that the body's competencies when it comes to legislative and budget matters were very weak, due to lack of expert staff.

He won 304 from the 382 votes through acclamation, with competitors such as Ali Masykur Musa, Saifullah Yusuf and Mohammad Mahfud MD.

[22] The Supreme Court also determined that the removal of Alwi Shihab was invalid in November 2005, strengthening the ulama faction's claims to party leadership.

[23] Despite this, the Ministry of Law and Human Rights recognized Iskandar's faction as legitimate in March 2006, followed by the South Jakarta District Court in June.

[31] On 25 December, he removed Gus Dur's sister Lily Wahid from the party, citing internal rule violations.

[44] Following major demonstrations by workers across the country in October 2012,[45] Iskandar created regulations regarding outsourcing, limiting it to 5 sectors i.e. mining, catering, transport, cleaning and security.

[55] For the presidential election, PKB under Iskandar backed PDI-P candidate Joko Widodo (Jokowi) who won and became president.

[59] He criticized Minister of Maritime Affairs and Fisheries Susi Pudjiastuti's policies, saying that they cause trouble for the Indonesian fishermen.

[61] On 26 March 2018, as part of a new regulation on the legislative bodies, he was appointed to one of three newly created deputy speaker positions in the MPR.

[67] When another occurrence happened later, PKB's deputy secretary general Daniel Johan claimed that the banners were put up by a grassroots movement.

[73] Other surveys conducted on similar dates however put forth other contenders such as Agus Harimurti Yudhoyono, if incumbent Jusuf Kalla is unaccounted for.

[74] On 15 March 2018, Iskandar announced that he had officially proposed to become Joko Widodo's running mate for 2019, citing his advantages as an attractor for Muslim voters.

[76] In August, Joko Widodo officially declared Indonesian Ulema Council leader Ma'ruf Amin as his vice presidential candidate.

As a response to the announcement, the Democratic Party under former president Susilo Bambang Yudhoyono withdrew its support of Baswedan's candidacy.

According to Iskandar, he called in four major political figures (Megawati Soekarnoputri, Taufiq Kiemas, Abdurrahman Wahid and Eros Djarot) to convince his in-laws when he proposed.