In 1920, Siddiqui proceeded to University College London to study medicine. However, after one year of pre-medical studies, he moved to Frankfurt University in 1921 to study chemistry. In 1924, he married his German classmate, Ethel Wilhelmina Schneeman. He received Doctor of Philosophy under the supervision of Prof Julius Von Braun in 1927. During his college days in Germany in the 1920s, Germany experienced high inflation and he went through some hard economic times. In these tough times, India's then eminent philanthropist Hakim Ajmal Khan used to send him Rupees400 every month. Many years later, as a successful scientist in Pakistan, Siddiqui repaid Hakeem Ajmal Khan's kindness by dedicating his discoveries after him.