Home Office data shows that across the four boroughs 108,790 people who applied to stay in the region under the EU Settlement Scheme have had their cases dealt with since Britain left the bloc.
Just 3,830 were refused permission to stay (3.5 per cent), while 90,460 were given either settled status, granting permanent residency, or pre-settled status, which allows them to stay for five years.
Nearly a quarter of all applications to live in the Black Country were from Romanians (24,700), while more than one fifth (21,250) came from Poles.
The scheme was launched in March 2019 to regulate the immigration status of European citizens who live in the UK.
The figures show nearly 33,000 EU citizens have been allowed to stay in Wolverhampton, while 28,070 have made their home in Sandwell.
In Walsall the figure was almost 20,000, and it was 9,780 in Dudley.
Under the scheme, applicants can appeal against rejection, but campaign group the3Million, said the system was leaving too many people "in limbo".
Policy and research officer Monique Hawkins, said: "Many people report not being able to get through to helplines, and find it next to impossible to get progress updates on their applications.
"For those who have been refused, the administrative review and appeals process face their own lengthy delays.
"We are extremely concerned about the length of time it is taking to unite people with their lawful status, and thereby their rights to continue living and working in the UK."
It comes after it emerged that more than 230,000 people had applied for settled status after the Government's June 30 deadline.
Across the Black Country, 4,600 applicants missed the cut off date, although the Government said those with a reasonable excuse would still be considered.
A Home Office spokeswoman said the scheme had been an "overwhelming success", with 6.3 million applications received and 5.5 million people being granted permission to stay so far.
She added: “Caseworkers will always look for reasons to grant rather than refuse.
"Individuals can be refused on eligibility or criminality grounds, and if a refused applicant disagrees with our decision, they can apply for an administrative review or appeal.
“We have published non-exhaustive guidance on reasonable grounds for making a late EUSS application and take a flexible and pragmatic approach to considering them, and we’ve made millions of pounds available in funding for organisations to support vulnerable applicants."