diff --git a/CHANGELOG.md b/CHANGELOG.md
index 898f544..cf731b3 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,6 +6,10 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 
 ## [Unreleased]
 
+### Added
+
+- Add support for custom taxonomies filtering ([#42](https://github.com/studiometa/wp-toolkit/issues/42), [#43](https://github.com/studiometa/wp-toolkit/pull/43), [ae541b5](https://github.com/studiometa/wp-toolkit/commit/ae541b5))
+
 ## v2.2.2 - 2024.04.19
 
 ### Fixed
@@ -49,9 +53,9 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 - Add an `EmailManager` to configure `PHPMailer` via environment variables ([#22](https://github.com/studiometa/wp-toolkit/pull/22))
 - Add `enqueue_script($handle, $path)` and `enqueue_style($handle, $path)` method to the `AssetsManager` class ([#23](https://github.com/studiometa/wp-toolkit/pull/23))
 - Add a `Plugin::disable` method to the `Plugin` helper class ([#26](https://github.com/studiometa/wp-toolkit/pull/26))
-- Add a `request` helper function  ([#26](https://github.com/studiometa/wp-toolkit/pull/26))
+- Add a `request` helper function ([#26](https://github.com/studiometa/wp-toolkit/pull/26))
 - Add a `Request` helper class ([#26](https://github.com/studiometa/wp-toolkit/pull/26))
-- Add a `env` helper function  ([#26](https://github.com/studiometa/wp-toolkit/pull/26))
+- Add a `env` helper function ([#26](https://github.com/studiometa/wp-toolkit/pull/26))
 - Add a `Env` helper class ([#26](https://github.com/studiometa/wp-toolkit/pull/26))
 
 ### Changed
diff --git a/src/Managers/FacetsManager.php b/src/Managers/FacetsManager.php
index db4e90c..5dc74d7 100644
--- a/src/Managers/FacetsManager.php
+++ b/src/Managers/FacetsManager.php
@@ -8,7 +8,6 @@
 namespace Studiometa\WPToolkit\Managers;
 
 use WP_Query;
-use Timber\Timber;
 use Twig\Environment;
 use Twig\TwigFunction;
 use Studiometa\WPToolkit\Managers\ManagerInterface;
@@ -63,9 +62,106 @@ public function add_facets_to_query(WP_Query &$query): void
             return;
         }
 
+        $tax_queries = [];
+        $regular_vars = [];
+
         foreach ($this->facets as $query_var => $value) {
-            $query->query_vars[ $query_var ] = $value;
+            $taxonomy_data = $this->parse_taxonomy_query_var($query_var);
+            
+            if ($taxonomy_data) {
+                $tax_queries[] = $this->build_tax_query($taxonomy_data, $value);
+            } else {
+                $regular_vars[$query_var] = $value;
+            }
+        }
+
+        // Apply regular query vars
+        foreach ($regular_vars as $query_var => $value) {
+            $query->query_vars[$query_var] = $value;
+        }
+
+        // Apply taxonomy queries
+        if (!empty($tax_queries)) {
+            $existing_tax_query = $query->get('tax_query', []);
+            if (!empty($existing_tax_query)) {
+                $tax_queries[] = $existing_tax_query;
+            }
+            $query->set('tax_query', $tax_queries);
+        }
+    }
+
+    /**
+     * Parse a query variable to determine if it's a taxonomy query.
+     *
+     * @param string $query_var The query variable name.
+     * @return array|null Array with taxonomy and operator data, or null if not a taxonomy query.
+     */
+    private function parse_taxonomy_query_var(string $query_var): ?array
+    {
+        $taxonomies = get_taxonomies(['public' => true]);
+        
+        // Direct taxonomy match
+        if (array_key_exists($query_var, $taxonomies)) {
+            return ['taxonomy' => $query_var, 'operator' => 'IN'];
+        }
+
+        // Check for suffixed taxonomy queries
+        $suffixes = ['__in', '__not_in', '__and', '__exists'];
+        foreach ($suffixes as $suffix) {
+            if (str_ends_with($query_var, $suffix)) {
+                $taxonomy = substr($query_var, 0, -strlen($suffix));
+                if (array_key_exists($taxonomy, $taxonomies)) {
+                    $operator = match ($suffix) {
+                        '__in' => 'IN',
+                        '__not_in' => 'NOT IN',
+                        '__and' => 'AND',
+                        '__exists' => 'EXISTS',
+                    };
+                    return ['taxonomy' => $taxonomy, 'operator' => $operator];
+                }
+            }
         }
+
+        return null;
+    }
+
+    /**
+     * Build a tax_query array for a given taxonomy and value.
+     *
+     * @param array $taxonomy_data Array with taxonomy and operator info.
+     * @param string|array $value The query value.
+     * @return array The tax_query array.
+     */
+    private function build_tax_query(array $taxonomy_data, string|array $value): array
+    {
+        $tax_query = [
+            'taxonomy' => $taxonomy_data['taxonomy'],
+            'operator' => $taxonomy_data['operator'],
+        ];
+
+        if ($taxonomy_data['operator'] === 'EXISTS') {
+            // EXISTS queries don't need terms/field
+            return $tax_query;
+        }
+
+        // Handle different value types
+        if (is_array($value)) {
+            $terms = $value;
+        } else {
+            $terms = array_map('trim', explode(',', $value));
+        }
+
+        // Determine if we're dealing with term IDs or slugs
+        $first_term = reset($terms);
+        if (is_numeric($first_term)) {
+            $tax_query['field'] = 'term_id';
+            $tax_query['terms'] = array_map('intval', $terms);
+        } else {
+            $tax_query['field'] = 'slug';
+            $tax_query['terms'] = $terms;
+        }
+
+        return $tax_query;
     }
 
     /**
diff --git a/tests/Managers/FacetsManagerTest.php b/tests/Managers/FacetsManagerTest.php
index 195811b..25e6236 100644
--- a/tests/Managers/FacetsManagerTest.php
+++ b/tests/Managers/FacetsManagerTest.php
@@ -51,4 +51,163 @@ public function test_it_should_add_a_twig_helper_function()
         $this->assertTrue($function instanceof TwigFunction);
         $this->assertTrue($function->getCallable()('cat') === 2);
     }
+
+    public function test_it_should_handle_taxonomy_queries_with_slugs()
+    {
+        // Register a test taxonomy
+        register_taxonomy('test_taxonomy', 'post', ['public' => true]);
+
+        request()->query->set('facets', ['test_taxonomy' => 'slug1,slug2']);
+        $manager = new FacetsManager();
+        $manager->run();
+
+        $this->go_to('/?facets[test_taxonomy]=slug1,slug2');
+        global $wp_query;
+
+        $tax_query = $wp_query->get('tax_query');
+        $this->assertIsArray($tax_query);
+        $this->assertCount(1, $tax_query);
+        $this->assertEquals('test_taxonomy', $tax_query[0]['taxonomy']);
+        $this->assertEquals('IN', $tax_query[0]['operator']);
+        $this->assertEquals('slug', $tax_query[0]['field']);
+        $this->assertEquals(['slug1', 'slug2'], $tax_query[0]['terms']);
+    }
+
+    public function test_it_should_handle_taxonomy_queries_with_ids()
+    {
+        register_taxonomy('test_taxonomy', 'post', ['public' => true]);
+
+        request()->query->set('facets', ['test_taxonomy' => '1,2,3']);
+        $manager = new FacetsManager();
+        $manager->run();
+
+        $this->go_to('/?facets[test_taxonomy]=1,2,3');
+        global $wp_query;
+
+        $tax_query = $wp_query->get('tax_query');
+        $this->assertEquals('term_id', $tax_query[0]['field']);
+        $this->assertEquals([1, 2, 3], $tax_query[0]['terms']);
+    }
+
+    public function test_it_should_handle_taxonomy_not_in_queries()
+    {
+        register_taxonomy('test_taxonomy', 'post', ['public' => true]);
+
+        request()->query->set('facets', ['test_taxonomy__not_in' => 'excluded-slug']);
+        $manager = new FacetsManager();
+        $manager->run();
+
+        $this->go_to('/?facets[test_taxonomy__not_in]=excluded-slug');
+        global $wp_query;
+
+        $tax_query = $wp_query->get('tax_query');
+        $this->assertEquals('test_taxonomy', $tax_query[0]['taxonomy']);
+        $this->assertEquals('NOT IN', $tax_query[0]['operator']);
+        $this->assertEquals(['excluded-slug'], $tax_query[0]['terms']);
+    }
+
+    public function test_it_should_handle_taxonomy_and_queries()
+    {
+        register_taxonomy('test_taxonomy', 'post', ['public' => true]);
+
+        request()->query->set('facets', ['test_taxonomy__and' => 'slug1,slug2']);
+        $manager = new FacetsManager();
+        $manager->run();
+
+        $this->go_to('/?facets[test_taxonomy__and]=slug1,slug2');
+        global $wp_query;
+
+        $tax_query = $wp_query->get('tax_query');
+        $this->assertEquals('AND', $tax_query[0]['operator']);
+    }
+
+    public function test_it_should_handle_taxonomy_exists_queries()
+    {
+        register_taxonomy('test_taxonomy', 'post', ['public' => true]);
+
+        request()->query->set('facets', ['test_taxonomy__exists' => '1']);
+        $manager = new FacetsManager();
+        $manager->run();
+
+        $this->go_to('/?facets[test_taxonomy__exists]=1');
+        global $wp_query;
+
+        $tax_query = $wp_query->get('tax_query');
+        $this->assertEquals('test_taxonomy', $tax_query[0]['taxonomy']);
+        $this->assertEquals('EXISTS', $tax_query[0]['operator']);
+        $this->assertArrayNotHasKey('terms', $tax_query[0]);
+        $this->assertArrayNotHasKey('field', $tax_query[0]);
+    }
+
+    public function test_it_should_combine_taxonomy_and_regular_queries()
+    {
+        register_taxonomy('test_taxonomy', 'post', ['public' => true]);
+
+        request()->query->set('facets', [
+            'test_taxonomy' => 'test-slug',
+            'meta_key' => 'custom_field',
+            'posts_per_page' => 5
+        ]);
+        $manager = new FacetsManager();
+        $manager->run();
+
+        $this->go_to('/?facets[test_taxonomy]=test-slug&facets[meta_key]=custom_field&facets[posts_per_page]=5');
+        global $wp_query;
+
+        // Check taxonomy query
+        $tax_query = $wp_query->get('tax_query');
+        $this->assertIsArray($tax_query);
+        $this->assertEquals('test_taxonomy', $tax_query[0]['taxonomy']);
+
+        // Check regular query vars
+        $this->assertEquals('custom_field', $wp_query->query_vars['meta_key']);
+        $this->assertEquals(5, $wp_query->query_vars['posts_per_page']);
+    }
+
+    public function test_it_should_handle_existing_tax_query()
+    {
+        register_taxonomy('test_taxonomy', 'post', ['public' => true]);
+
+        request()->query->set('facets', ['test_taxonomy' => 'new-slug']);
+        $manager = new FacetsManager();
+        $manager->run();
+
+        // Set up existing tax_query
+        $existing_tax_query = [
+            [
+                'taxonomy' => 'category',
+                'field' => 'slug',
+                'terms' => ['existing-category'],
+                'operator' => 'IN'
+            ]
+        ];
+
+        $this->go_to('/?facets[test_taxonomy]=new-slug');
+        global $wp_query;
+        $wp_query->set('tax_query', $existing_tax_query);
+
+        // Trigger the facets query modification
+        $manager->add_facets_to_query($wp_query);
+
+        $tax_query = $wp_query->get('tax_query');
+        $this->assertCount(2, $tax_query);
+        $this->assertEquals('test_taxonomy', $tax_query[0]['taxonomy']);
+        $this->assertEquals('category', $tax_query[1][0]['taxonomy']);
+    }
+
+    public function test_it_should_handle_array_values_in_facets()
+    {
+        register_taxonomy('test_taxonomy', 'post', ['public' => true]);
+
+        request()->query->set('facets', ['test_taxonomy' => ['slug1', 'slug2']]);
+        $manager = new FacetsManager();
+        $manager->run();
+
+        $this->go_to('/?facets[test_taxonomy][]=slug1&facets[test_taxonomy][]=slug2');
+        global $wp_query;
+
+        $tax_query = $wp_query->get('tax_query');
+        $this->assertEquals(['slug1', 'slug2'], $tax_query[0]['terms']);
+        $this->assertEquals('slug', $tax_query[0]['field']);
+    }
 }