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When applying for a spouse visa, does the fact that we haven't officially lived together yet affect our application? We have met and stayed together a couple of times before we got married and stayed together for a month after our wedding.
It doesn't. For married couples what matters is to be able to prove that the relationship is genuine. Proof that common travel, or attendance to family gatherings, etc., is all good proof.
Your husband can apply for an EEA Family Permit till 30 June.