[JSWolf]

Originally Posted by DNSB

Hardly relevant since the OP is likely to pick an indent they prefer.

An alternative in the CSS stylesheet to indent all but first paragraphs might be:

p { 
    text-indent: 1.5em; 
}

p:first-of-type {
    text-indent: 0;
}

Use the Extra CSS options to insert this.

Going off a vague memory, I took a quick look at the Layout options in conversion and there seems to be a setting to insert an indent when removing spacing between paragraphs. See the attached image.

But if you want your ePub to also be backwards compatible with ePub2, then you cannot use p:first-of-type. However, if you do as I do and use <h2>chapter header</h2> then you can use...

h2 + p {
  text-indent; 0;
}