My partner (23) is from Lithuania and didn’t apply for his EU settlement status by the deadline as he wasn’t aware it was something he had to complete.
He has lived in England since he was 5 years old (so for 18 years now) and we have a 2 year old together who was born in England and I am an English citizen.
He has now applied 3 times past the deadline and had told them that this was something he wasn’t aware he had to complete and every time has been declined as they have asked him for evidence as to why he is late to applying and he can’t prove that he simply didn’t know this was a requirement.
Without his EUSS he can lose his right to work and rent in the UK and we are not sure what we are suppose to do about this as the helplines are offering us 0 help on how to work around this.
This has become an extremely stressful situation for us and we can not afford to pay for visas and indefinite leave to remain.
Does anyone have any better knowledge on this or has gone through this too and knows what can be done.
TIA
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Unfortunately if the HO already rejected his application, he doesn't have much leg to stand on. The only recourse would be judicial review, but I have a feeling this might be more costly than the ILR.
I am on a spousal visa and on my Leave to remain and due to apply for ILR next year.

Maybe get married in front of the magistrates?

he won't automatically get settled status by marriage. He still has to apply for a visa. Considering he has lived in the UK for more than 5 years, it will be Indefinite To Remain and the cost is around £2,400 with extra documents and evidence of their relationship.

You can apply for ILR and fill in the form to get the fee waived. I don't know the criteria for that, might need to read up on that. While he is waiting for the decision for his ILR, all his rights remain until the decision is made.