I should note, the specific error I am getting when trying to do anything is:

WARNING: wp-includes/functions.php:1378 - mkdir(): Permission denied

On my installation php5-fpm has 'www-data' as the user. Also my htdocs folder belong to the user 'www-data' and the permission is set to 755

In my www.conf file in /etc/php5/fpm/pool.d/ I have set the user to www-data yet for someone reason it's still running under my user.

Anyone have any ideas on how I can fix this?

Try

sudo chown -R www-data:www-data /var/www

From what I understand.. The instruction in the article https://www.digitalocean.com/community/articles/how-to-install-wordpress-with-nginx-on-ubuntu-12-04

"Give ownership of the directory to the nginx user, replacing the "username" with the name of your server user.

sudo chown www-data:www-data * -R
sudo usermod -a -G www-data username"

reverts ownership to you as the user rather than www:data

try to revert it back to www-data.

Thanks for that leoadhemartan, so from what I understood of your reply, I ran:
sudo usermod -a -G www-data www-data
Which I'm assuming sets the ownership to the www-data user, however restarting the php5-fpm shows that my user is still the one running it (as opposed to www-data).

What am I doing wrong?

taking a wild guess..

are you using the Duplicator plugin?

I tried that on my first droplet a few months ago, I quit because of issues with PHP. I decided to manually upload the backup (ftp the files, load the db through mysql).

Hi,

I am not, I'm using BackWPup. Regardless of plugin, I'm sure that the process running under the wrong user can cause problems and I'd like to try and fix it anyway if possible.

Can you pastebin php5-fpm's config file and the output of the following two commands?

sudo service php5-fpm restart

sudo ps wwaux | grep php5-fpm