Went Edge Quarry will continue its mining operations close to Brockadale Nature Reserve which accommodates a number of rare species and is classed as a site of special scientific interest (SSSI).
People from Pontefract, including Darrington Parish Council, were among 250 who were strongly opposed the scheme, citing the loss of green space and perceived threat to wildlife in the area.
But the quarry's managers argued the expansion was badly needed to meet the demand for housebuilding materials - an argument also contested by the objectors.
The developers also promised to restore the affected site to grassland by 2032, in a move they claimed will result in a "biodiversity net gain" for the area.
North Yorkshire County councillors voted in favour of the application on Tuesday.
Reacting to the verdict, the chair of Darrington Parish Council, Michael Britton said he was "very concerned".
"Brockadale Nature Reserve is one of the most beautiful parts of our area," he said.
"Although it's not within our parish boundary, so many of our parishioners use it for all sorts of activities - walking their dogs, picnicking and taking their families there.
"It just seems so wrong to do it to that area and I can't think of a site that should be better protected.
Celia Loughran, who until standing down this month represented the Pontefract South ward on Wakefield Council, was similarly critical of the expansion.
"It's very disappointing for the people who will be affected by this and the environment," she said.
"When are people going to wake up to the serious problems faced by the natural world and the ways this will impact a special local area?"
The Yorkshire Wildlife Trust and conservation charity Plant Life had also objected to the scheme.
They told councillors that Brockadale is home to rare species of flora, insects and snails which could be harmed by the expansion.
The reserve is used by universities in York and Leeds for biology field trips, such is its unique nature, the meeting was told.
However, representing Went Edge Quarry, planning agent John Carlon said any impact on wildlife would be minimised and limited.
He also said the expansion would benefit the local economy to the value of £2m.
Mr Carlon said: "There is little or no risk to the SSSI from the expansion of quarrying that cannot be managed.
"The unique habitat of woodland and calcareous meadow will remain, as will the rare species of flora.
"There are many civil engineering contractors who source limestone from this quarry and they've provided letters of support.
"They are concerned there will be a large shortage of limestone because Barnsdale Bar and Darrington Quarries cannot meet the demand.
"There are projects that have already been postponed in the Leeds City Region and in York because of a shortage of primary aggregates."
After a debate lasting four hours, the council's planning committee voted six to three in favour of approving the expansion.
Local Democracy Reporting Service