ImageMagick is converting only the first page of the pdf

You can use one commandline with two commands (gs, convert) connected through a pipe, if the first command can write its output to stdout, and if the second one can read its input from stdin.

1. Luckily, gs can write to stdout (... -o %stdout ...).
2. Luckily, convert can read from stdin (convert -background transparent - output.png).

Problem solved:

• GS used for alpha channel handling a special image,
• convert used for creating transparent background,
• pipe used to avoid writing out a temp file on disk.

Complete solution:

gs -sDEVICE=pngalpha       \
   -o %stdout              \
   -r144 cover.pdf         \
   |                       \
convert                    \
   -background transparent \
   -                       \
    cover.png

Update

If you want to have a separate PNG per PDF page, you can use the %d syntax:

gs -sDEVICE=pngalpha -o file-%03d.png -r144 cover.pdf

This will create PNG files named page-000.png, page-001.png, ... (Note that the %d-counting is zero-based -- file-000.png corresponds to page 1 of the PDF, 001 to page 2...

Or, if you want to keep your transparent background, for a 100-page PDF, do

for i in {1..100}; do        \
                             \
  gs -sDEVICE=pngalpha       \
     -dFirstPage="${i}"      \
     -dLastPage="${i}"       \
     -o %stdout              \
     -r144 input.pdf         \
     |                       \
  convert                    \
     -background transparent \
     -                       \
      page-${i}.png ;        \
                             \
done

convert multipage.tiff -density 300x300 -compress jpeg multipage.pdf

This should work, though there can be some issues.