diff --git a/.wp-env.json b/.wp-env.json
index 858e671e80..a38fb9d76c 100644
--- a/.wp-env.json
+++ b/.wp-env.json
@@ -46,7 +46,8 @@
         "wp-content/plugins/unsupported-elasticsearch-version.php": "./tests/e2e/src/wordpress-files/test-plugins/unsupported-elasticsearch-version.php",
         "wp-content/plugins/multiple-required-features.php": "./tests/e2e/src/wordpress-files/test-plugins/multiple-required-features.php",
         "wp-content/uploads/content-example.xml": "./tests/e2e/src/wordpress-files/test-docs/content-example.xml",
-        "wp-content/plugins/echo-shortcode.php": "./tests/e2e/src/wordpress-files/test-plugins/echo-shortcode.php"
+        "wp-content/plugins/echo-shortcode.php": "./tests/e2e/src/wordpress-files/test-plugins/echo-shortcode.php",
+        "wp-content/plugins/custom-search-form.php": "./tests/e2e/src/wordpress-files/test-plugins/custom-search-form.php"
       }
     }
   }
diff --git a/assets/js/api-search/src/reducer.js b/assets/js/api-search/src/reducer.js
index b4250ac862..f17757044b 100644
--- a/assets/js/api-search/src/reducer.js
+++ b/assets/js/api-search/src/reducer.js
@@ -34,7 +34,7 @@ export default (state, action) => {
 			newState.args = { ...newState.args, ...args, offset: 0 };
 			newState.isOn = true;
 
-			if (updateDefaults && args.post_type.length) {
+			if (updateDefaults && args.post_type?.length) {
 				newState.argsSchema.post_type.default = args.post_type;
 			}
 
diff --git a/assets/js/instant-results/apps/modal.js b/assets/js/instant-results/apps/modal.js
index 648b807bcd..f894591ed7 100644
--- a/assets/js/instant-results/apps/modal.js
+++ b/assets/js/instant-results/apps/modal.js
@@ -8,8 +8,8 @@ import { __ } from '@wordpress/i18n';
  * Internal dependencies.
  */
 import { useApiSearch } from '../../api-search';
-import { facets } from '../config';
-import { getPostTypesFromForm } from '../utilities';
+import { argsSchema, facets } from '../config';
+import { getArgsFromForm } from '../utilities';
 import Modal from '../components/common/modal';
 import Layout from '../components/layout';
 
@@ -59,11 +59,10 @@ export default () => {
 				return;
 			}
 
-			const { value } = inputRef.current;
-			const post_type = getPostTypesFromForm(inputRef.current.form);
+			const args = getArgsFromForm(inputRef.current.form, argsSchema);
 			const updateDefaults = !facets.some((f) => f.name === 'post_type');
 
-			search({ post_type, search: value, updateDefaults });
+			search({ ...args, updateDefaults });
 		},
 		[inputRef, search],
 	);
diff --git a/assets/js/instant-results/utilities.js b/assets/js/instant-results/utilities.js
index af15c4b02f..37027cfed4 100644
--- a/assets/js/instant-results/utilities.js
+++ b/assets/js/instant-results/utilities.js
@@ -1,3 +1,13 @@
+/**
+ * WordPress dependencies.
+ */
+import { applyFilters } from '@wordpress/hooks';
+
+/**
+ * Internal dependencies.
+ */
+import { sanitizeArg } from '../api-search/src/utilities';
+
 /**
  * Format a date.
  *
@@ -27,21 +37,62 @@ export const formatPrice = (number, options) => {
 };
 
 /**
- * Get the post types from a search form.
+ * Get search args from a search form for Instant Results.
  *
- * @param {HTMLFormElement} form Form element.
- * @returns {Array} Post types.
+ * @param {HTMLFormElement} form       Form element.
+ * @param {object}          argsSchema Search args schema.
+ * @returns {object} Search args.
  */
-export const getPostTypesFromForm = (form) => {
-	const data = new FormData(form);
+export const getArgsFromForm = (form, argsSchema) => {
+	/**
+	 * Filter the map of query variable names to Instant Results arg names.
+	 *
+	 * @filter ep.instantResults.queryVarMap
+	 * @since 5.4.0
+	 *
+	 * @param {object} map Map of WordPress query var names to Instant Results arg names.
+	 * @param {HTMLFormElement} form Form element.
+	 * @param {object} argsSchema Search args schema.
+	 * @returns {object} Map of WordPress query var names to Instant Results arg names.
+	 */
+	const QUERY_VAR_MAP = applyFilters(
+		'ep.instantResults.queryVarMap',
+		{
+			s: 'search',
+			cat: 'tax-category',
+			tag_id: 'tax-post_tag',
+		},
+		{ form, argsSchema },
+	);
+
+	const formData = new FormData(form);
+	const params = new URLSearchParams();
+	const formEntries = Array.from(formData.entries());
 
-	if (data.has('post_type')) {
-		return data.getAll('post_type').slice(-1);
-	}
+	formEntries.forEach(([key, value]) => {
+		// Strip trailing [] from array-style field names.
+		const cleanKey = key.replace(/\[\]$/, '');
+		// Resolve the EP arg name: explicit map → direct schema match → tax- prefix.
+		const argName =
+			QUERY_VAR_MAP[cleanKey] ||
+			(argsSchema[cleanKey] ? cleanKey : null) ||
+			(argsSchema[`tax-${cleanKey}`] ? `tax-${cleanKey}` : null);
+
+		if (value && argName) {
+			const existing = params.get(argName);
+			params.set(argName, existing ? `${existing},${value}` : value);
+		}
+	});
 
-	if (data.has('post_type[]')) {
-		return data.getAll('post_type[]');
-	}
+	return Object.entries(argsSchema).reduce((args, [arg, options]) => {
+		const param = params.get(arg);
+		if (param !== null) {
+			const value = sanitizeArg(param, options, false);
+			if (value !== null) {
+				args[arg] = value;
+			}
+		}
 
-	return [];
+		return args;
+	}, {});
 };
diff --git a/tests/e2e/src/specs/instant-results.spec.ts b/tests/e2e/src/specs/instant-results.spec.ts
index 6a40945cbc..d01c9e3a42 100644
--- a/tests/e2e/src/specs/instant-results.spec.ts
+++ b/tests/e2e/src/specs/instant-results.spec.ts
@@ -26,12 +26,20 @@ test.describe('Instant Results Feature', { tag: '@group1' }, () => {
 		});
 	};
 
-	const addInstantResultFilter = async (page: Page, filterName: string) => {
+	const addInstantResultFilter = async (
+		page: Page,
+		filterName: string,
+		options?: { keepExisting?: boolean },
+	) => {
 		await page.locator('.components-form-token-field__input').focus();
-		await page.keyboard.press('Backspace');
-		await page.keyboard.press('Backspace');
-		await page.keyboard.press('Backspace');
-		await page.keyboard.press('Backspace');
+
+		if (!options?.keepExisting) {
+			await page.keyboard.press('Backspace');
+			await page.keyboard.press('Backspace');
+			await page.keyboard.press('Backspace');
+			await page.keyboard.press('Backspace');
+		}
+
 		await page.locator('.components-form-token-field__input').fill(filterName);
 		await page.keyboard.press('ArrowDown');
 		await page.keyboard.press('Enter');
@@ -598,6 +606,58 @@ test.describe('Instant Results Feature', { tag: '@group1' }, () => {
 					'wpCli',
 				);
 			});
+
+			test('Is possible to search with taxonomies and tags in search form', async ({
+				loggedInPage,
+			}) => {
+				await maybeEnableFeature('instant-results');
+				await activatePlugin(loggedInPage, 'custom-search-form', 'wpCli');
+
+				await goToAdminPage(loggedInPage, 'admin.php?page=elasticpress');
+				const apiResponsePromise = loggedInPage.waitForResponse(
+					'**/wp-json/elasticpress/v1/features*',
+				);
+
+				await loggedInPage.getByRole('button', { name: 'Live Search' }).click();
+				await loggedInPage.getByRole('button', { name: 'Instant Results' }).click();
+				await addInstantResultFilter(loggedInPage, '(category)');
+				await addInstantResultFilter(loggedInPage, '(post_tag)', {
+					keepExisting: true,
+				});
+				await loggedInPage.getByRole('button', { name: 'Save changes' }).click();
+
+				await apiResponsePromise;
+
+				await publishPost(
+					loggedInPage,
+					{
+						title: 'Custom Search Form Page',
+						content: '[ep_custom_search_form]',
+					},
+					true,
+				);
+
+				await expect(loggedInPage.locator('form.searchform')).toBeVisible();
+				await expect(loggedInPage.locator('form.searchform input[name="s"]')).toBeVisible();
+				await expect(
+					loggedInPage.locator('form.searchform .search-tags-checkboxes'),
+				).toBeVisible();
+
+				const responsePromise = instantResultRequestPromise(loggedInPage, 'search=');
+
+				await loggedInPage.locator('#cat').selectOption({ label: 'aciform' });
+				await loggedInPage.locator('form.searchform').getByLabel('edge case').check();
+				await loggedInPage.locator('form.searchform').getByLabel('categories').check();
+				await loggedInPage.locator('#searchform #s').click();
+				await loggedInPage.keyboard.press('Enter');
+
+				await expect(loggedInPage.locator('.ep-search-modal')).toBeVisible();
+				await responsePromise;
+
+				await expect(loggedInPage.locator('.ep-search-tokens')).toContainText('aciform');
+				await expect(loggedInPage.locator('.ep-search-tokens')).toContainText('edge case');
+				await expect(loggedInPage.locator('.ep-search-tokens')).toContainText('categories');
+			});
 		});
 
 		test('Is possible to filter the arguments schema', async ({ loggedInPage }) => {
diff --git a/tests/e2e/src/wordpress-files/test-plugins/custom-search-form.php b/tests/e2e/src/wordpress-files/test-plugins/custom-search-form.php
new file mode 100644
index 0000000000..b43ffc2c42
--- /dev/null
+++ b/tests/e2e/src/wordpress-files/test-plugins/custom-search-form.php
@@ -0,0 +1,72 @@
+<?php
+/**
+ * Plugin Name: Custom Search Form
+ * Description: Custom search form for test purposes.
+ * Version:     1.0.0
+ * Author:      10up Inc.
+ * License:     GPLv2 or later
+ *
+ * @package ElasticPress_Tests_E2e
+ */
+
+/**
+ * Shortcode for custom search form with category dropdown and tag checkboxes.
+ *
+ * @return string HTML output for the search form.
+ */
+function ep_custom_search_form_shortcode() {
+	ob_start();
+	?>
+	<form role="search" method="get" id="searchform" class="searchform" action="<?php echo esc_url( home_url( '/' ) ); ?>">
+		<label class="screen-reader-text" for="s"><?php esc_html_e( 'Search for:', 'custom-search-form' ); ?></label>
+		<input type="search" value="<?php echo esc_attr( get_search_query() ); ?>" name="s" id="s" placeholder="<?php esc_attr_e( 'Search…', 'custom-search-form' ); ?>" />
+		<?php
+		wp_dropdown_categories(
+			[
+				'show_option_all' => __( 'All Categories', 'custom-search-form' ),
+				'name'            => 'cat',
+			],
+		);
+		$tag_terms = get_terms(
+			[
+				'taxonomy'   => 'post_tag',
+				'hide_empty' => true,
+			],
+		);
+		?>
+		<fieldset class="search-tags-checkboxes">
+			<legend><?php esc_html_e( 'Filter by Tags:', 'custom-search-form' ); ?></legend>
+			<?php
+			foreach ( $tag_terms as $term ) :
+				?>
+				<label>
+					<input type="checkbox" name="custom_tag_id[]" value="<?php echo esc_attr( $term->term_id ); ?>" />
+					<?php echo esc_html( $term->name ); ?>
+				</label><br />
+			<?php endforeach; ?>
+		</fieldset>
+		<input type="submit" id="searchsubmit" value="<?php esc_attr_e( 'Search', 'custom-search-form' ); ?>" />
+	</form>
+	<?php
+	return ob_get_clean();
+}
+add_shortcode( 'ep_custom_search_form', 'ep_custom_search_form_shortcode' );
+
+/**
+ * Filter the Instant Results query variable map.
+ */
+add_action(
+	'wp_footer',
+	function (): void {
+		?>
+	<script>
+		document.addEventListener('DOMContentLoaded', function() {
+			wp.hooks.addFilter('ep.instantResults.queryVarMap', 'ep-test', (queryVarMap) => {
+				queryVarMap['custom_tag_id'] = 'tax-post_tag';
+				return queryVarMap;
+			});
+		});
+	</script>
+		<?php
+	}
+);