In Arabic, the word Sakinah means peace or tranquility. Allah uses this word in the Qur’aan in two ways.
Allah says in Surah Al-Fath (48:4):
هو الذي أنزل السكينة في قلوب المؤمنين ليزدادوا إيمانا مع إيمانه
These ayahs were revealed after the disbelievers prevented the Prophet sallallahu ‘alayhi wa sallam from making ‘Umrah in Makkah. Here, Allah uses the word fee, which means “in” or “into”. “He it is Who sent down As-Sakinah (calmness and tranquillity) into the hearts of the believers, that they may grow more in Faith along with their (present) Faith…”
Allah says in Surah At-Tawbah (9:26):
ثم أنزل الله سكينته على رسوله و على المؤمنين
These ayahs were revealed about a battle (the battle of Hunayn). Here, Allah uses the word ‘ala, which means “on”. “Then Allah did send down His Sakinah (calmness, tranquillity and reassurance, etc.) on the Messenger (Muhammad SAW), and on the believers…”
In the first instance, the believers must have been frustrated and angry because they were prevented from making ‘Umrah. Thus, Allah sent sakinah into their hearts. The peace had to come from within in this emotional state.
In the second instance, there was fear from the outside. They needed protection and security in a physical sense. In times of fear, we need sakeenah on us. Hence, Allah says that He sent sakinah onto the believers.
Depending on the situation, Allah uses these different words. Even though the difference in the wording is just a preposition, there is such depth to the meaning. SubhaanAllah.