From: Fatāwā ʿUlamāʾ-e-Ḥadīth, Kitāb al-Ṣalāh, Volume 1, Pages 148–149
It is not allowed to perform Sunnah or any missed obligatory prayer once the Iqāmah has been called. The Messenger of Allah ﷺ said:
"When the Iqāmah is called for a prayer, then only the prayer for which the Iqāmah is called should be performed."
(Aḥmad and others)
Hence, one should not perform the Fajr Sunnahs once the Iqāmah has started.
If someone misses the Fajr Sunnahs due to the ongoing congregation, then they may offer these Sunnahs after the Fajr (farḍ) prayer and before sunrise.
This is supported by narrations from Ibn Ḥibbān, Ibn Khuzaymah, al-Bayhaqī, al-Tirmidhī, and Abū Dāwūd, from Qays ibn ʿAmr ibn Sahl al-Anṣārī.
(Muḥaddith Dehlī, Volume 9, Issue 12)
❀ Question
If someone joins the congregational Fajr prayer but misses the Sunnah prayers, when should they offer those Sunnahs? Some people say that one should separate from the congregation, pray the Sunnahs, and then join the Jamaʿah.❀ Answer
If a person arrives at the mosque while the Fajr congregation has already started, or the Iqāmah has been called, then it is not permissible to perform the Sunnah prayers at that time — not in the row, not separately, not behind a pillar or inside a chamber, nor outside the mosque.It is not allowed to perform Sunnah or any missed obligatory prayer once the Iqāmah has been called. The Messenger of Allah ﷺ said:
"When the Iqāmah is called for a prayer, then only the prayer for which the Iqāmah is called should be performed."
(Aḥmad and others)
Hence, one should not perform the Fajr Sunnahs once the Iqāmah has started.
If someone misses the Fajr Sunnahs due to the ongoing congregation, then they may offer these Sunnahs after the Fajr (farḍ) prayer and before sunrise.
This is supported by narrations from Ibn Ḥibbān, Ibn Khuzaymah, al-Bayhaqī, al-Tirmidhī, and Abū Dāwūd, from Qays ibn ʿAmr ibn Sahl al-Anṣārī.
(Muḥaddith Dehlī, Volume 9, Issue 12)