diff --git a/api.wordpress.org/public_html/dotorg/github/activity.php b/api.wordpress.org/public_html/dotorg/github/activity.php
index f8ca79e7cc..7ab9d5f1cc 100644
--- a/api.wordpress.org/public_html/dotorg/github/activity.php
+++ b/api.wordpress.org/public_html/dotorg/github/activity.php
@@ -43,7 +43,16 @@
 function get_signed_payload_or_die() {
 	$payload            = file_get_contents( 'php://input' );
 	// Validate that the request came from GitHub.
-	$sent_signature     = $_SERVER['HTTP_X_HUB_SIGNATURE_256'];
+	$sent_signature     = (string) filter_var(
+		wp_unslash( $_SERVER['HTTP_X_HUB_SIGNATURE_256'] ?? '' ),
+		FILTER_VALIDATE_REGEXP,
+		[
+			'options' => [
+				'regexp'  => '/^sha256=[0-9a-f]{64}\z/i',
+				'default' => '',
+			],
+		]
+	);
 	$expected_signature = 'sha256=' . hash_hmac( 'sha256', $payload, constant( 'GH_ACTIVITY_WEBHOOK_SECRET' ) );
 
 	if ( ! hash_equals( $expected_signature, $sent_signature ) ) {
@@ -71,7 +80,7 @@ function github_user_to_user_id( $user ) {
 	return $user_id ? intval( $user_id ) : false;
 }
 
-$event   = $_SERVER['HTTP_X_GITHUB_EVENT'];
+$event   = sanitize_key( wp_unslash( $_SERVER['HTTP_X_GITHUB_EVENT'] ?? '' ) );
 $payload = get_signed_payload_or_die();
 
 // Ignore anything on private repos.
@@ -163,6 +172,7 @@ function github_user_to_user_id( $user ) {
 	case 'issues':
 		if ( ! in_array( $payload->action, [ 'opened', 'edited', 'closed', 'deleted' ] ) ) {
 			header( 'HTTP/1.0 422 Unprocessable Entity', true, 422 );
+			// phpcs:ignore WordPress.Security.EscapeOutput.OutputNotEscaped -- Plain-text response body; the endpoint sends Content-Type: text/plain.
 			die( "NO; $event:{$payload->action} not required." );
 		}
 
@@ -215,6 +225,7 @@ function github_user_to_user_id( $user ) {
 
 		if ( ! in_array( $payload->action, [ 'opened', 'reopened', 'edited', 'closed' ] ) ) {
 			header( 'HTTP/1.0 422 Unprocessable Entity', true, 422 );
+			// phpcs:ignore WordPress.Security.EscapeOutput.OutputNotEscaped -- Plain-text response body; the endpoint sends Content-Type: text/plain.
 			die( "NO; $event:{$payload->action} not required." );
 		}
 
diff --git a/api.wordpress.org/public_html/dotorg/helpscout/common.php b/api.wordpress.org/public_html/dotorg/helpscout/common.php
index 92fc0c12f3..ef30866683 100644
--- a/api.wordpress.org/public_html/dotorg/helpscout/common.php
+++ b/api.wordpress.org/public_html/dotorg/helpscout/common.php
@@ -22,18 +22,27 @@ function load_wordpress( $wp_init_host = '' ) {
  * Retrieve the incoming payload, and verify it's from HelpScout.
  */
 function get_request() {
-	global $HTTP_RAW_POST_DATA;
-
 	// HelpScout sends json data in the POST, so grab it from the input directly.
-	$HTTP_RAW_POST_DATA = file_get_contents( 'php://input' );
-
-	// Check the signature matches.
-	if ( ! is_from_helpscout( $HTTP_RAW_POST_DATA, $_SERVER['HTTP_X_HELPSCOUT_SIGNATURE'] ?? '' ) ) {
+	$raw_post_data = file_get_contents( 'php://input' );
+
+	// Check the signature matches. It's a base64 encoded HMAC, allowing for the URL-safe alphabet.
+	$signature = (string) filter_var(
+		wp_unslash( $_SERVER['HTTP_X_HELPSCOUT_SIGNATURE'] ?? '' ),
+		FILTER_VALIDATE_REGEXP,
+		[
+			'options' => [
+				'regexp'  => '!^[A-Za-z0-9+/=_-]+\z!',
+				'default' => '',
+			],
+		]
+	);
+
+	if ( ! is_from_helpscout( $raw_post_data, $signature ) ) {
 		exit;
 	}
 
 	// get the info from HS.
-	return json_decode( $HTTP_RAW_POST_DATA );
+	return json_decode( $raw_post_data );
 }
 
 // function to verify signature from HelpScout
diff --git a/api.wordpress.org/public_html/dotorg/helpscout/plugins-themes.php b/api.wordpress.org/public_html/dotorg/helpscout/plugins-themes.php
index 5ca6231eb9..810056609b 100644
--- a/api.wordpress.org/public_html/dotorg/helpscout/plugins-themes.php
+++ b/api.wordpress.org/public_html/dotorg/helpscout/plugins-themes.php
@@ -66,7 +66,7 @@
 	] );
 
 	if ( $post_ids ) {
-		echo '<p><strong>' . ucwords( $type ) . ' mentioned in this email:</strong></p>';
+		echo '<p><strong>' . esc_html( ucwords( $type ) ) . ' mentioned in this email:</strong></p>';
 
 		display_items( $post_ids );
 
@@ -84,7 +84,7 @@
 		$items = get_user_items( $user );
 		if ( $items ) {
 			$url = add_query_arg( [ 'post_type' => $repo_post_types[ $type ], 'author' => $user->ID ], admin_url( 'edit.php' ) );
-			echo '<p><strong><a href="' . esc_url( $url ) . '">' . ucwords( $type ) . ' owned by this user:</a></strong></p>';
+			echo '<p><strong><a href="' . esc_url( $url ) . '">' . esc_html( ucwords( $type ) ) . ' owned by this user:</a></strong></p>';
 
 			display_items( $items );
 
diff --git a/api.wordpress.org/public_html/dotorg/helpscout/webhook.php b/api.wordpress.org/public_html/dotorg/helpscout/webhook.php
index c2ff332d00..4a6be57bc8 100644
--- a/api.wordpress.org/public_html/dotorg/helpscout/webhook.php
+++ b/api.wordpress.org/public_html/dotorg/helpscout/webhook.php
@@ -8,7 +8,7 @@
 
 // $request is the validated HelpScout request.
 $request = get_request();
-$event   = $_SERVER['HTTP_X_HELPSCOUT_EVENT'] ?? '';
+$event   = sanitize_text_field( wp_unslash( $_SERVER['HTTP_X_HELPSCOUT_EVENT'] ?? '' ) );
 
 // Warm the caches.
 get_email_thread( $request->id, true );
diff --git a/api.wordpress.org/public_html/dotorg/trac/mentions-handler.php b/api.wordpress.org/public_html/dotorg/trac/mentions-handler.php
index 151b1008a4..cd93618418 100644
--- a/api.wordpress.org/public_html/dotorg/trac/mentions-handler.php
+++ b/api.wordpress.org/public_html/dotorg/trac/mentions-handler.php
@@ -1,4 +1,14 @@
 <?php
+/**
+ * Trac comment mentions handler: creates notifications for mentioned users.
+ *
+ * This endpoint is called by Trac, not by a browser: requests are authenticated by the
+ * shared URL_SECRET__MENTIONS secret posted alongside the payload, not by a user session.
+ *
+ * phpcs:disable WordPress.Security.NonceVerification
+ *
+ * @package WordPressdotorg\API\Trac
+ */
 
 define( 'BLOCKED',    0 );
 define( 'SUBSCRIBED', 1 );
@@ -7,12 +17,21 @@
 require dirname( dirname( __DIR__ ) ) . '/wp-init.php';
 require dirname( dirname( __DIR__ ) ) . '/includes/slack-config.php';
 
-if ( ! isset( $_POST['secret'] ) || $_POST['secret'] !== \Dotorg\Slack\Trac\URL_SECRET__MENTIONS ) {
+if ( ! is_string( $_POST['secret'] ?? null ) || ! hash_equals( \Dotorg\Slack\Trac\URL_SECRET__MENTIONS, wp_unslash( $_POST['secret'] ) ) ) {
 	exit;
 }
 
+if ( ! isset( $_POST['payload'] ) || ! is_string( $_POST['payload'] ) ) {
+	exit;
+}
+
+// phpcs:ignore WordPress.Security.ValidatedSanitizedInput.InputNotSanitized -- JSON document parsed by json_decode() below; text sanitization would corrupt it.
 $payload = json_decode( wp_unslash( $_POST['payload'] ) );
 
+if ( ! is_object( $payload ) ) {
+	exit;
+}
+
 require_once WP_PLUGIN_DIR . '/wporg-notifications.php';
 $notif = WPOrg_Notifications::get_instance();
 
diff --git a/api.wordpress.org/public_html/dotorg/trac/oembed/index.php b/api.wordpress.org/public_html/dotorg/trac/oembed/index.php
index bbcaaf678e..39d9be13cf 100644
--- a/api.wordpress.org/public_html/dotorg/trac/oembed/index.php
+++ b/api.wordpress.org/public_html/dotorg/trac/oembed/index.php
@@ -15,7 +15,15 @@
  * oEmbed Discovery is not enabled, as although adding the tag to trac is possible, it requires inline Javascript.
  * 
  * Please do not abuse this API, otherwise an API KEY will become required.
+ *
+ * This is a public, unauthenticated, stateless oEmbed endpoint: requests are anonymous
+ * GET requests from arbitrary sites, so there is no session or nonce to verify.
+ *
+ * phpcs:disable WordPress.Security.NonceVerification
+ *
+ * @package WordPressdotorg\API\Trac
  */
+
 include dirname( dirname( dirname( __DIR__ ) ) ) . '/wp-init.php';
 
 // Avoid warnings from DomDocument.
@@ -24,8 +32,8 @@
 // Mark this as an oEmbed response for caching.
 header( 'X-WP-Embed: true' );
 
-$url = $_GET['url'] ?? '';
-$url = is_string( $url ) ? wp_unslash( $url ) : '';
+// Control characters only; percent-encoding or stripping `%` would corrupt the URLs matched below.
+$url = (string) filter_var( wp_unslash( $_GET['url'] ?? '' ), FILTER_UNSAFE_RAW, FILTER_FLAG_STRIP_LOW );
 
 header( 'Allow: GET' );
 header( 'Expires: ' . gmdate( 'D, d M Y H:i:s \G\M\T', time() + HOUR_IN_SECONDS ), true );
@@ -38,6 +46,7 @@
 
 if (
 	! $url ||
+	! isset( $_SERVER['REQUEST_METHOD'] ) ||
 	'GET' !== $_SERVER['REQUEST_METHOD'] ||
 	! in_array( strtolower( (string) wp_parse_url( $url, PHP_URL_HOST ) ), $allowed_hosts, true )
 ) {
@@ -100,7 +109,7 @@
 	);
 
 	if ( ! empty( $_GET['api_key'] ) ) {
-		$embed_url = add_query_arg( 'api_key', wp_unslash( $_GET['api_key'] ), $embed_url );
+		$embed_url = add_query_arg( 'api_key', sanitize_text_field( wp_unslash( $_GET['api_key'] ) ), $embed_url );
 	}
 
 	$embed_url .= '#el=' . $id;
@@ -143,6 +152,7 @@
 
 $cache_key = sha1( $url );
 if ( $data = wp_cache_get( $cache_key, 'trac-oembed' ) ) {
+	// phpcs:ignore WordPress.Security.EscapeOutput.OutputNotEscaped -- Cached copy of the HTML document generated below; this endpoint serves text/html.
 	die( $data );
 }
 
@@ -166,6 +176,7 @@
 ) {
 	$output = '<h1>Temporarily Unavailable</h1>';
 	wp_cache_set( $cache_key, $output, 'trac-oembed', MINUTE_IN_SECONDS );
+	// phpcs:ignore WordPress.Security.EscapeOutput.OutputNotEscaped -- Static HTML markup defined above; this endpoint serves text/html.
 	die( $output );
 }
 
@@ -324,4 +335,5 @@ function send() {
 
 wp_cache_set( $cache_key, $data, 'trac-oembed', HOUR_IN_SECONDS );
 
+// phpcs:ignore WordPress.Security.EscapeOutput.OutputNotEscaped -- Complete HTML document built by DOMDocument above; this endpoint serves text/html and escaping it would destroy the markup.
 echo $data;
\ No newline at end of file
diff --git a/api.wordpress.org/public_html/dotorg/trac/pr/class-trac.php b/api.wordpress.org/public_html/dotorg/trac/pr/class-trac.php
index 6cb9e65a62..adfdda2d31 100644
--- a/api.wordpress.org/public_html/dotorg/trac/pr/class-trac.php
+++ b/api.wordpress.org/public_html/dotorg/trac/pr/class-trac.php
@@ -148,6 +148,7 @@ protected function _api( $method, $params ) {
 			$json = $this->trac_json_deobjectify( $json );
 
 		} elseif ( $json && isset( $json->error ) ) {
+			// phpcs:ignore WordPress.Security.EscapeOutput.ExceptionNotEscaped -- Discarded by every catch site or logged as plain text; escaping would corrupt the log line.
 			throw new \Exception( 'JSON Error: ' . $json->error->code . ' ' . $json->error->message );
 		} elseif ( ! $json ) {
 			throw new \Exception( 'Trac API Error: Trac Unavailable.' );
diff --git a/api.wordpress.org/public_html/dotorg/trac/pr/index.php b/api.wordpress.org/public_html/dotorg/trac/pr/index.php
index 5010171352..ec89771b31 100644
--- a/api.wordpress.org/public_html/dotorg/trac/pr/index.php
+++ b/api.wordpress.org/public_html/dotorg/trac/pr/index.php
@@ -1,15 +1,23 @@
 <?php
+/**
+ * Trac endpoint for GitHub pull request data attached to tickets.
+ *
+ * This is a public, unauthenticated, read-only JSON endpoint consumed by Trac: requests are
+ * anonymous GET requests, so there is no session or nonce to verify.
+ *
+ * phpcs:disable WordPress.Security.NonceVerification
+ *
+ * @package WordPressdotorg\API\Trac
+ */
+
 namespace WordPressdotorg\API\Trac\GithubPRs;
 
 require dirname( dirname( dirname( __DIR__ ) ) ) . '/wp-init.php';
 require __DIR__ . '/functions.php';
 
-$trac          = $_GET['trac'] ?? '';
-$trac          = is_string( $trac ) ? $trac : '';
-$trac          = preg_replace( '![^a-z]!', '', $trac );
+$trac          = preg_replace( '![^a-z]!', '', sanitize_key( wp_unslash( $_GET['trac'] ?? '' ) ) );
 $ticket        = intval( $_GET['ticket'] ?? 0 );
-$author        = wp_unslash( $_GET['author'] ?? '' );
-$author        = is_string( $author ) ? $author : '';
+$author        = sanitize_text_field( wp_unslash( $_GET['author'] ?? '' ) );
 $authenticated = ! empty( $_GET['authenticated'] ); // Longer caches for logged out requests.
 
 header( 'Content-Type: application/json' );
diff --git a/api.wordpress.org/public_html/dotorg/trac/pr/webhook.php b/api.wordpress.org/public_html/dotorg/trac/pr/webhook.php
index 3e2515e157..b88ea43db9 100644
--- a/api.wordpress.org/public_html/dotorg/trac/pr/webhook.php
+++ b/api.wordpress.org/public_html/dotorg/trac/pr/webhook.php
@@ -1,4 +1,16 @@
 <?php
+/**
+ * GitHub webhook receiver for pull request events.
+ *
+ * This endpoint is a GitHub webhook receiver: requests are authenticated by the
+ * `X-Hub-Signature` HMAC computed with GH_PRBOT_WEBHOOK_SECRET, not by a user session,
+ * so there is no nonce to verify.
+ *
+ * phpcs:disable WordPress.Security.NonceVerification
+ *
+ * @package WordPressdotorg\API\Trac
+ */
+
 namespace WordPressdotorg\API\Trac\GithubPRs;
 
 require dirname( dirname( dirname( __DIR__ ) ) ) . '/wp-init.php';
@@ -12,10 +24,20 @@ function verify_signature() {
 
 	// Validate that the request came from GitHub.
 	if ( ! defined( 'GH_PRBOT_WEBHOOK_SECRET' ) ) {
-		return;
+		header( 'HTTP/1.0 500 Internal Server Error', true, 500 );
+		die( 'Webhook secret not configured.' );
 	}
 
-	$sent_signature     = $_SERVER['HTTP_X_HUB_SIGNATURE'] ?? '';
+	$sent_signature     = (string) filter_var(
+		wp_unslash( $_SERVER['HTTP_X_HUB_SIGNATURE'] ?? '' ),
+		FILTER_VALIDATE_REGEXP,
+		[
+			'options' => [
+				'regexp'  => '/^sha1=[0-9a-f]{40}\z/i',
+				'default' => '',
+			],
+		]
+	);
 	$expected_signature = 'sha1=' . hash_hmac( 'sha1', $HTTP_RAW_POST_DATA, GH_PRBOT_WEBHOOK_SECRET );
 
 	if ( ! hash_equals( $expected_signature, $sent_signature ) ) {
@@ -33,11 +55,12 @@ function verify_signature() {
 
 $payload = json_decode( $HTTP_RAW_POST_DATA );
 
-if ( ! empty( $_GET['trac'] ) ) {
-	define( 'WEBHOOK_TRAC_HINT', $_GET['trac'] );
+$trac_hint = sanitize_key( wp_unslash( $_GET['trac'] ?? '' ) );
+if ( $trac_hint ) {
+	define( 'WEBHOOK_TRAC_HINT', $trac_hint );
 }
 
-switch ( $_SERVER['HTTP_X_GITHUB_EVENT'] ) {
+switch ( sanitize_key( wp_unslash( $_SERVER['HTTP_X_GITHUB_EVENT'] ?? '' ) ) ) {
 	// Pull Request
 	case 'pull_request':