Pagination not working on custom template.

Do you use a query on the loop?

Well, you can see everything I have up in the loop there in the pastebin link, but this is my main query:

<?php
if (is_home()) {
query_posts("cat=-94"."&posts_per_page=9");}?>
<?php $c = 1; //init counter
$bpr = 3; //boxes per row
if(have_posts()) :
	while(have_posts()) :
		the_post();?>

Try to do it without the query_posts:

But with something like this in your functions.php

function my_home_query( $query ) {
  // not an admin page and is the main query
  if (!is_admin() && $query->is_main_query()){
    if(is_home()){
     //cat=-94"."&posts_per_page=9
      $query->set('cat', -94);
      $query->set('posts_per_page', 9);

    }
  }
}
add_action( 'pre_get_posts', 'my_home_query' );

Basically it’s more reliable and faster. read here why: https://developer.wordpress.com/2012/05/14/querying-posts-without-query_posts/

Aha! You are a genius! Thanks so much for this! You saved me countless hours, and headaches. E-cookie?

Just one (okay, two) things before you go –

I am using this below to generate the pagination:

<?php global $wp_query;
$big = 999999999; // need an unlikely integer
echo paginate_links( array(
    'base' => str_replace( $big, '%#%', esc_url( get_pagenum_link( $big ) ) ),
    'format' => '?paged=%#%',
    'current' => max( 1, get_query_var('paged') ),
    'total' => $wp_query->max_num_pages
) );?>

Will this (and your fix) also work on all of my custom Page templates?
And, can the Next Previous links be changed to images?

Thanks so much!

By custom page templates you mean this with a query_posts in it?
https://codex.www.ads-software.com/Pages#Creating_Your_Own_Page_Templates

let me see about the images.

Put a folder called “images” with the images in it in your theme in a folder .

Add this to the paginate_links arguments array:

'next_text' => '<img src="'.get_template_directory_uri().'/images/next.png" alt="previous page" />',
'prev_text' => '<img src="'.get_template_directory_uri().'/images/previous.png" alt="next page" />',

in this example the images are called “next.png” and “previous.png”.

https://codex.www.ads-software.com/Function_Reference/paginate_links

Yes, that’s exactly right. For instance, every link you see on my navigation (https://ohmybonbon.com) utilizes a custom page template.

So, for my page template in the “Beauty” cagetory, I am using this query:

<?php query_posts('category_name='.beauty.','.makeup.'&post_status=publish,future');?>

So, I have a feeling this isn’t quite going to work the same. I’m sure the solution is probably easy, and staring me in the face, but I’m a little brain dead this morning.

You have been a tremendous help! I will try adding the previous and next arguments.

If you don’t use the main loop to show the content of the Page I would use a new WP_Query in stead of a query_posts.
https://codex.www.ads-software.com/Function_Reference/WP_Query

example loop:

$the_query = new WP_Query( 'category_name='.beauty.','.makeup.'&post_status=publish,future' );
if($the_query->have_posts()) :
while ( $the_query->have_posts() ) : $the_query->the_post();
// rest of loop
endwhile;
endif;

But, this means you have to change the paginate_links arguments [untested]:

<?php 

$big = 999999999; // need an unlikely integer
echo paginate_links( array(
    'base' => str_replace( $big, '%#%', esc_url( get_pagenum_link( $big ) ) ),
    'format' => '?paged=%#%',
    'current' => max( 1, get_query_var('paged') ),

    //  I changed this
    'total' => $the_query->max_num_pages
) );?>

On all other pages (category.php, search.php etc..) where you want to alter the main loop try it with the pre_get_post action hook with conditional tags in functions.php

keesiemeijer, you have been a tremendous help! I have everything pretty well how I want it, now. I am going to tamper with the pagination style a bit, but it works splendidly now, thanks to you!