Flamborough Bird Observatory says the hide, south of the Fog Station, is needed to protect people carrying out sea watches in the worst weather.
But locals argued that the stretch of unspoilt Heritage Coast should not be developed.
However members of East Riding Council’s eastern area planning committee voted eight to two in favour of the plans for the single-storey hide.
The FBO welcomed the news but admitted there was “bridge-building” to do with locals.
Secretary Tony Hood said the data they gathered fed into organisations like the RSPB and Yorkshire Wildlife Trust, and could be escalated up through Natural England, influencing Government policy. The application and getting the hide built will cost £40,000.
He said: “It is a massive step forward for the Observatory.
“Having a focal point on the headland is going to give us an opportunity to engage with the public and the local community. We do have some bridge-building to do. We are more than willing to talk to people.
“We are aware it is a contentious area where it is and we haven’t taken this lightly. This has been years in the planning.”
However objector Andrew Barden, who spoke at the meeting, said the hide was a “huge expense” and insisted it would only be needed a few days a year. He added: “I do feel disappointed, but we ended up with nearly 70 objections - all local people - and I was very pleased that people do care and don’t want these things to spoil what is a beautiful coast.”