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I have a rasterStack object in R and a set of polygons that represent different landcover classes in that area. For all the cells that fall in those polygons, I have extracted pixel values for each band and saved these in a dataframe. However, I can't get the centroid coordinates for these cells and I need them. Any advice on how to achieve that?

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You can use xyFromCell

library(raster)
r <- raster(ncols=5, nrows=5)
cells <- c(3, 7, 10)
xyFromCell(r, cells)
#       x  y
#[1,]   0 72
#[2,] -72 36
#[3,] 144 36

If you wanted the coordinates for all cells, you could do

xy <- xyFromCell(r, 1:ncell(r))

or

xy <- coordinates(raster(r))

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