Pandoc uses the UTF-8 character encoding for both input and output.
If your local character encoding is not UTF-8, you should pipe input and
output through iconv
:
iconv -t utf-8 input.txt | pandoc | iconv -f utf-8
Note that in some output formats (such as HTML, LaTeX, ConTeXt, RTF,
OPML, DocBook, and Texinfo), information about the character encoding is
included in the document header, which will only be included if you use
the -s/--standalone
option.