When Rasulullah s.a. did hijrat (migrated from Makkah to Madina), Rasulullah s.a. halted at a place name Quba, where Rasulullah s.a. constructed a masjid.
After a period of 1-1/2 years Rasulullah s.a. was asked to rotate the Qibla from Masjid ul Aqsaa towards Masjid ul Haram. This farman came in this masjid.
This is why Masjid e Quba is also famous as Masjid ul Qiblatain (masjid with two Qiblas)