diff --git a/pipelines/batch/pom.xml b/pipelines/batch/pom.xml
index d6479ee52..a00e741ab 100644
--- a/pipelines/batch/pom.xml
+++ b/pipelines/batch/pom.xml
@@ -41,7 +41,7 @@
     <maven-surefire-plugin.version>3.5.3</maven-surefire-plugin.version>
     <nemo.version>0.1</nemo.version>
     <flink.artifact.name>beam-runners-flink-1.14</flink.artifact.name>
-    <mysql.driver.version>8.0.30</mysql.driver.version>
+    <mysql.driver.version>9.3.0</mysql.driver.version>
     <postgresql.version>42.7.7</postgresql.version>
 
   </properties>
@@ -73,8 +73,8 @@
     <!--JDBC specific dependencies-->
 
     <dependency>
-      <groupId>mysql</groupId>
-      <artifactId>mysql-connector-java</artifactId>
+      <groupId>com.mysql</groupId>
+      <artifactId>mysql-connector-j</artifactId>
       <version>${mysql.driver.version}</version>
       <!-- We need to exclude this to avoid the clash with the same dependency under the artifact
       org.apache.beam:beam-sdks-java-io-google-cloud-platform so that it does not end up in
diff --git a/pipelines/common/pom.xml b/pipelines/common/pom.xml
index 2d7c1788e..b229af588 100644
--- a/pipelines/common/pom.xml
+++ b/pipelines/common/pom.xml
@@ -143,7 +143,7 @@
     <dependency>
       <groupId>org.apache.parquet</groupId>
       <artifactId>parquet-avro</artifactId>
-      <version>1.13.1</version>
+      <version>1.15.2</version>
     </dependency>
 
     <!-- TODO: This is in the dependencies of the above with "provided" scope.
diff --git a/pipelines/controller/pom.xml b/pipelines/controller/pom.xml
index 50fde9374..e11ed8523 100644
--- a/pipelines/controller/pom.xml
+++ b/pipelines/controller/pom.xml
@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!--
 
-    Copyright 2020-2024 Google LLC
+    Copyright 2020-2025 Google LLC
 
     Licensed under the Apache License, Version 2.0 (the "License");
     you may not use this file except in compliance with the License.
@@ -30,7 +30,7 @@
 
   <properties>
     <java.version>17</java.version>
-    <spring-boot.version>3.2.2</spring-boot.version>
+    <spring-boot.version>3.5.3</spring-boot.version>
   </properties>
 
   <dependencyManagement>
@@ -85,6 +85,11 @@
       <groupId>io.micrometer</groupId>
       <artifactId>micrometer-registry-prometheus</artifactId>
     </dependency>
+    <dependency>
+      <groupId>io.prometheus</groupId>
+      <artifactId>simpleclient</artifactId>
+      <version>0.16.0</version>
+    </dependency>
 
     <!-- This is to make it easier to hot-swap static content, i.e., to make
      testing static content changes in a running server easier. -->
diff --git a/pipelines/controller/src/main/java/com/google/fhir/analytics/metrics/PipelineMetricsEndpoint.java b/pipelines/controller/src/main/java/com/google/fhir/analytics/metrics/PipelineMetricsEndpoint.java
index 6c1c0e81f..42b6a0643 100644
--- a/pipelines/controller/src/main/java/com/google/fhir/analytics/metrics/PipelineMetricsEndpoint.java
+++ b/pipelines/controller/src/main/java/com/google/fhir/analytics/metrics/PipelineMetricsEndpoint.java
@@ -1,5 +1,5 @@
 /*
- * Copyright 2020-2023 Google LLC
+ * Copyright 2020-2025 Google LLC
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -26,8 +26,6 @@
 import org.springframework.boot.actuate.endpoint.annotation.Endpoint;
 import org.springframework.boot.actuate.endpoint.annotation.ReadOperation;
 import org.springframework.boot.actuate.endpoint.web.WebEndpointResponse;
-import org.springframework.boot.actuate.endpoint.web.annotation.WebEndpoint;
-import org.springframework.stereotype.Component;
 import org.springframework.util.MimeType;
 import org.springframework.util.MimeTypeUtils;
 
@@ -35,12 +33,14 @@
  * This is a custom implementation of the spring actuator {@link Endpoint @Endpoint} which exports
  * only the pipeline metrics in a format that can be scraped by the Prometheus server.
  */
-@WebEndpoint(id = "pipeline-metrics")
-@Component
+// @WebEndpoint(id = "pipeline-metrics")
+// @Component
 public class PipelineMetricsEndpoint {
 
   private static final int METRICS_SCRAPE_CHARS_EXTRA = 1024;
 
+  // The CollectorRegistry @Bean is removed after Spring 3.2.2 so this component needs to be fixed
+  // (see PrometheusMetricsExportAutoConfiguration).
   private final CollectorRegistry collectorRegistry;
 
   private volatile int nextMetricsScrapeSize = 16;