I found out that I just needed to add a meta tag with charset attribute to my HTML code:
import pdfkit
html_content = """
<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8">
</head>
<body>
<p>€</p>
<p>áéíóúñö</p>
<body>
</html>
"""
pdfkit.from_string(html_content, 'out.pdf')
I actually spent quite some time following wrong solutions like the one suggested here. In case someone is interested, I wrote a short story on my blog. Sorry for the SPAM :)