Applying programmatically a coupon to an Order in WooCommerce3

// Create the coupon
global $woocommerce;
$coupon = new WC_Coupon($coupon_code);

// Get the coupon discount amount (My coupon is a fixed value off)
$discount_total = $coupon->get_amount();

// Loop through products and apply the coupon discount
foreach($order->get_items() as $order_item){
    $product_id = $order_item->get_product_id();

    if($this->coupon_applies_to_product($coupon, $product_id)){
        $total = $order_item->get_total();
        $order_item->set_subtotal($total);
        $order_item->set_total($total - $discount_total);
        $order_item->save();
    }
}
$order->save();

// Add the coupon to the order
$item = new WC_Order_Item_Coupon();
$item->set_props(array('code' => $coupon_code, 'discount' => $discount_total, 'discount_tax' => 0));
$order->add_item($item);
$order->save();

/**
 * Apply a coupon to the order and recalculate totals.
 *
 * @since 3.2.0
 * @param string|WC_Coupon $raw_coupon Coupon code or object.
 * @return true|WP_Error True if applied, error if not.
 */
public function apply_coupon( $raw_coupon )

$user = wp_get_current_user();

$order = new WC_Order();
$order->set_status('completed');
$order->set_customer_id($user->ID);
$order->add_product($product , 1); // This is an existing SIMPLE product
$order->set_currency( get_woocommerce_currency() );
$order->set_prices_include_tax( 'yes' === get_option( 'woocommerce_prices_include_tax' ) );
$order->set_customer_ip_address( WC_Geolocation::get_ip_address() );
$order->set_customer_user_agent( wc_get_user_agent() );
$order->set_address([
    'first_name' => $user->first_name,
    'email'      => $user->user_email,
], 'billing' );
// $order->calculate_totals();  // You don't need this

$order->apply_coupon($coupon_code);

$order->save();