Thanks to the answers I have figured out that I am unable to use fetch_all() because i am using PHP 5.2.17 - fetch_assoc with while loop worked.
The function I am using fetch_all is coming back with this error: 
Fatal error: Call to undefined method mysqli_result::fetch_all() in
$mysqli = new mysqli($host, $username, $password, $database);
$query = "LONG QUERY that works, tested in phpmyadmin"
$result = $mysqli->query($query);
$result->fetch_all(); or  $mysqli->fetch_all() tried both
mysqli_fetch_all() was already tried.
$mysqli->close(); 
I am able to connect to the DB and I have pulled single rows. When I place the query in PHPMYADMIN I get 5 rows back.
Does this function even work? Is there a way I can place my data into an assoc array on my own?
This function is available since PHP 5.3.0. Possibly your version is older. Use fetch_assoc() instead.
while ($row = $result->fetch_assoc()) {
    // do what you need.
}
                        The typical way to construct an associative array is in a while loop:
$results_array = array();
$result = $mysqli->query($query);
while ($row = $result->fetch_assoc()) {
  $results_array[] = $row;
}
                        Issue seems to be 'mysqli' and 'mysqlnd' are not working together. I had the same issue in cpanel
Steps:
1) Go to CPanel dashboard
2) Go to 'Select PHP Version', you should see a bunch of checkboxes
3) Set PHP version (5.4 or above)
4) Uncheck the 'mysqli' extension and check both 'mysqlind' and 'nd_mysqli'
Apparently 'nd_mysqli' is 'mysqli' but configured to work with 'mysqlind' and to make it work you have to uncheck 'mysqli' due to settings conflicts.
Following answer I found here helped me.
mysqli::fetch_all() needs mysqlnd driver to be installed before you can use it.
Please be careful about using fetch_all():
http://www.php.net/manual/en/mysqli-result.fetch-all.php#88031
Read the note about mysqldn requirement.
As an addition to Fabrizios answer, please consider building up your array with a loop:
$array = array();
while($row = $result->fetch_assoc())
    $array[] = $row;
                        If you don't want to iterate using Karolis' answer,
use 
     while($row = mysqli_fetch_array($result,MYSQLI_ASSOC))
    {
       $rows[] = $row;
    }
to achieve the same result as
$rows = mysqli_fetch_all($result, MYSQLI_ASSOC);
You may change constant to MYSQLI_NUM or MYSQLI_BOTH.
This optional parameter are  constants indicating what type of array should be produced from the current row data.
Notice that mysqli_fetch_array($result,MYSQLI_ASSOC ) behaves identically to the mysqli_fetch_assoc() function, while mysqli_fetch_array($result,MYSQLI_NUM) will behave identically to the mysqli_fetch_row() function. The final option MYSQLI_BOTH will create a single array with the attributes of both.
http://php.net/manual/en/mysqli-result.fetch-array.php
I had 5.6 but didn't work for me anyway. By enabling the mysqlnd driver it worked for me. Just write apt-get install php5-mysqlnd then restart php and you're good to go!
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