IslamQA
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Summary (from the source)
If you have already prayed one rak`ah with its two prostrations, then you should complete your prayer quickly. But if the khatib starts his khutbah before you have completed the first rak`ah with its two prostrations, then you should stop your prayer.
Question
If a person is praying two rak`ahs on Friday (at Jumu`ah) then the imam comes in, should he stop praying or not?
Answer
Praise be to Allah, and blessings and peace be upon the Messenger of Allah:
It seems to me, and Allah knows best, that if you have already prayed one rak`ah with its two prostrations, then you should complete your prayer quickly, because of the hadith of Abu Hurayrah (may Allah be pleased with him), that the Prophet (peace and blessings of Allah be upon him) said: “Whoever catches up with one rak`ah of the prayer has caught up with the prayer.” (Agreed upon).
But if the khatib starts his khutbah before you have completed the first rak`ah with its two prostrations, then you should stop your prayer, because of the obligation to listen to the khatib .
And Allah knows best.
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