diff --git a/aws-bundle/build.gradle b/aws-bundle/build.gradle
index 5b9054812a50..f9d356a774f5 100644
--- a/aws-bundle/build.gradle
+++ b/aws-bundle/build.gradle
@@ -44,7 +44,7 @@ project(":iceberg-aws-bundle") {
 
   shadowJar {
     archiveClassifier.set(null)
-    zip64 true
+    zip64 = true
 
     // include the LICENSE and NOTICE files for the shaded Jar
     from(projectDir) {
diff --git a/azure-bundle/build.gradle b/azure-bundle/build.gradle
index 0bdc30fdaa7e..25a1e4c856fe 100644
--- a/azure-bundle/build.gradle
+++ b/azure-bundle/build.gradle
@@ -32,7 +32,7 @@ project(":iceberg-azure-bundle") {
 
   shadowJar {
     archiveClassifier.set(null)
-    zip64 true
+    zip64 = true
 
     // include the LICENSE and NOTICE files for the shaded Jar
     from(projectDir) {
diff --git a/baseline.gradle b/baseline.gradle
index 7884c1a65ae3..c4cea08c7507 100644
--- a/baseline.gradle
+++ b/baseline.gradle
@@ -36,7 +36,6 @@ subprojects {
 
   // Thus we concede to applying all of the Baseline plugins individually on all the projects we are
   // ready to enforce linting on.
-  apply plugin: 'org.inferred.processors'
   if (!project.hasProperty('quick')) {
     apply plugin: 'com.palantir.baseline-checkstyle'
     apply plugin: 'com.palantir.baseline-error-prone'
diff --git a/bom/build.gradle b/bom/build.gradle
new file mode 100644
index 000000000000..3579f7b5df9c
--- /dev/null
+++ b/bom/build.gradle
@@ -0,0 +1,20 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied.  See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ */
+
+// This file is intentionally minimal - BOM configuration is in root build.gradle
\ No newline at end of file
diff --git a/build.gradle b/build.gradle
index 2c6ba9da2e06..9c0bc87100db 100644
--- a/build.gradle
+++ b/build.gradle
@@ -29,7 +29,6 @@ buildscript {
     classpath 'com.gradleup.shadow:shadow-gradle-plugin:8.3.9'
     classpath 'com.palantir.baseline:gradle-baseline-java:6.90.0'
     classpath 'com.diffplug.spotless:spotless-plugin-gradle:8.2.1'
-    classpath 'gradle.plugin.org.inferred:gradle-processors:3.7.0'
     classpath 'me.champeau.jmh:jmh-gradle-plugin:0.7.3'
     classpath 'gradle.plugin.io.morethan.jmhreport:gradle-jmh-report:0.9.6'
     classpath "com.github.alisiikh:gradle-scalastyle-plugin:3.5.0"
@@ -250,7 +249,7 @@ subprojects {
       } else {
         events "failed"
       }
-      exceptionFormat "full"
+      exceptionFormat = "full"
     }
 
     systemProperty 'project.version', project.version
@@ -285,7 +284,7 @@ project(':iceberg-bundled-guava') {
   shadowJar {
     archiveClassifier.set(null)
     configurations = [project.configurations.compileClasspath]
-    zip64 true
+    zip64 = true
 
     // include the LICENSE and NOTICE files for the shaded Jar
     from(projectDir) {
@@ -440,7 +439,7 @@ project(':iceberg-data') {
   test {
     useJUnitPlatform()
     // Only for TestSplitScan as of Gradle 5.0+
-    maxHeapSize '1500m'
+    maxHeapSize = '1500m'
   }
 }
 
@@ -618,9 +617,23 @@ project(':iceberg-delta-lake') {
   test {
     useJUnitPlatform()
   }
-  configurations {
-    integrationImplementation.extendsFrom testImplementation
-    integrationRuntime.extendsFrom testRuntimeOnly
+
+  // The newest version of delta-core uses Spark 3.5.*. Define integration source set and config
+  // before dependencies so integrationImplementation exists when dependencies are applied.
+  if (sparkVersions.contains("3.5")) {
+    sourceSets {
+      integration {
+        java.srcDir "$projectDir/src/integration/java"
+        resources.srcDir "$projectDir/src/integration/resources"
+        compileClasspath += main.output + test.output
+        runtimeClasspath += main.output + test.output
+      }
+    }
+
+    configurations {
+      integrationImplementation.extendsFrom testImplementation
+      integrationRuntime.extendsFrom testRuntimeOnly
+    }
   }
 
   dependencies {
@@ -671,15 +684,6 @@ project(':iceberg-delta-lake') {
   // The newest version of delta-core uses Spark 3.5.*. The integration test should only be built
   // if iceberg-spark-3.5 is available
   if (sparkVersions.contains("3.5")) {
-    sourceSets {
-      integration {
-        java.srcDir "$projectDir/src/integration/java"
-        resources.srcDir "$projectDir/src/integration/resources"
-        compileClasspath += main.output + test.output
-        runtimeClasspath += main.output + test.output
-      }
-    }
-
     task integrationTest(type: Test) {
       useJUnitPlatform()
       testClassesDirs = sourceSets.integration.output.classesDirs
@@ -1041,7 +1045,8 @@ project(':iceberg-open-api') {
   dependencies {
     testImplementation project(':iceberg-api')
     testImplementation project(':iceberg-core')
-    testImplementation project(':iceberg-core').sourceSets.test.runtimeClasspath
+    testImplementation project(path: ':iceberg-core', configuration: 'testArtifacts')
+    testImplementation project(path: ':iceberg-api', configuration: 'testArtifacts')
     testImplementation(testFixtures(project(':iceberg-open-api')))
 
     testImplementation libs.junit.jupiter
@@ -1125,7 +1130,7 @@ project(':iceberg-open-api') {
     archiveClassifier.set(null)
     configurations = [project.configurations.testFixturesRuntimeClasspath]
     from sourceSets.testFixtures.output
-    zip64 true
+    zip64 = true
 
     // include the LICENSE and NOTICE files for the runtime Jar
     from(projectDir) {
diff --git a/deploy.gradle b/deploy.gradle
index 740d0056273b..9b3313350abc 100644
--- a/deploy.gradle
+++ b/deploy.gradle
@@ -33,13 +33,13 @@ subprojects {
       task sourceJar(type: Jar, dependsOn: classes) {
         archiveClassifier.set('sources')
         from sourceSets.main.allSource
-        group 'build'
+        group = 'build'
       }
 
       task javadocJar(type: Jar, dependsOn: javadoc) {
         archiveClassifier.set('javadoc')
         from javadoc.destinationDir
-        group 'build'
+        group = 'build'
       }
 
       task testJar(type: Jar) {
@@ -124,8 +124,8 @@ subprojects {
       repositories {
         maven {
           credentials {
-            username project.hasProperty('mavenUser') ? "$mavenUser" : ""
-            password project.hasProperty('mavenPassword') ? "$mavenPassword" : ""
+            username = project.hasProperty('mavenUser') ? "$mavenUser" : ""
+            password = project.hasProperty('mavenPassword') ? "$mavenPassword" : ""
           }
           // upload to the releases repository using ./gradlew -Prelease publish
           def apacheSnapshotsRepoUrl = 'https://repository.apache.org/content/repositories/snapshots'
diff --git a/flink/v1.20/build.gradle b/flink/v1.20/build.gradle
index 3591bf37b1a7..a82b3db064c7 100644
--- a/flink/v1.20/build.gradle
+++ b/flink/v1.20/build.gradle
@@ -176,14 +176,16 @@ project(":iceberg-flink:iceberg-flink-runtime-${flinkMajorVersion}") {
     // all of those dependencies are required because the integration test extends FlinkTestBase
     integrationCompileOnly project(':iceberg-api')
     integrationImplementation libs.assertj.core
+    integrationImplementation libs.junit.jupiter
+    integrationImplementation libs.junit.platform.launcher
     integrationImplementation project(path: ":iceberg-flink:iceberg-flink-${flinkMajorVersion}", configuration: "testArtifacts")
     integrationImplementation project(path: ':iceberg-api', configuration: 'testArtifacts')
     integrationImplementation project(path: ':iceberg-hive-metastore', configuration: 'testArtifacts')
     integrationImplementation(libs.flink120.test.utils) {
       exclude group: "org.apache.curator", module: 'curator-test'
-      exclude group: 'junit'
     }
 
+    integrationImplementation libs.flink120.connector.base
     integrationImplementation libs.flink120.table.api.java.bridge
     integrationImplementation "org.apache.flink:flink-table-planner_${scalaVersion}:${libs.versions.flink120.get()}"
 
@@ -226,7 +228,7 @@ project(":iceberg-flink:iceberg-flink-runtime-${flinkMajorVersion}") {
   shadowJar {
     configurations = [project.configurations.runtimeClasspath]
 
-    zip64 true
+    zip64 = true
 
     // include the LICENSE and NOTICE files for the shaded Jar
     from(projectDir) {
@@ -255,6 +257,9 @@ project(":iceberg-flink:iceberg-flink-runtime-${flinkMajorVersion}") {
   task integrationTest(type: Test) {
     description = "Test Flink Runtime Jar against Flink ${flinkMajorVersion}"
     group = "verification"
+    useJUnitPlatform {
+      excludeEngines "junit-vintage"
+    }
     jvmArgs += project.property('extraJvmArgs')
     testClassesDirs = sourceSets.integration.output.classesDirs
     classpath = sourceSets.integration.runtimeClasspath + files(shadowJar.archiveFile.get().asFile.path)
diff --git a/flink/v2.0/build.gradle b/flink/v2.0/build.gradle
index 5907f41b3544..7bfc6387f75b 100644
--- a/flink/v2.0/build.gradle
+++ b/flink/v2.0/build.gradle
@@ -181,9 +181,9 @@ project(":iceberg-flink:iceberg-flink-runtime-${flinkMajorVersion}") {
     integrationImplementation project(path: ':iceberg-hive-metastore', configuration: 'testArtifacts')
     integrationImplementation(libs.flink20.test.utils) {
       exclude group: "org.apache.curator", module: 'curator-test'
-      exclude group: 'junit'
     }
 
+    integrationImplementation libs.flink20.connector.base
     integrationImplementation libs.flink20.table.api.java.bridge
     integrationImplementation "org.apache.flink:flink-table-planner_${scalaVersion}:${libs.versions.flink20.get()}"
 
@@ -226,7 +226,7 @@ project(":iceberg-flink:iceberg-flink-runtime-${flinkMajorVersion}") {
   shadowJar {
     configurations = [project.configurations.runtimeClasspath]
 
-    zip64 true
+    zip64 = true
 
     // include the LICENSE and NOTICE files for the shaded Jar
     from(projectDir) {
diff --git a/flink/v2.1/build.gradle b/flink/v2.1/build.gradle
index 91081bdc2e42..b17a275b16ec 100644
--- a/flink/v2.1/build.gradle
+++ b/flink/v2.1/build.gradle
@@ -176,14 +176,16 @@ project(":iceberg-flink:iceberg-flink-runtime-${flinkMajorVersion}") {
     // all of those dependencies are required because the integration test extends FlinkTestBase
     integrationCompileOnly project(':iceberg-api')
     integrationImplementation libs.assertj.core
+    integrationImplementation libs.junit.jupiter
+    integrationImplementation libs.junit.platform.launcher
     integrationImplementation project(path: ":iceberg-flink:iceberg-flink-${flinkMajorVersion}", configuration: "testArtifacts")
     integrationImplementation project(path: ':iceberg-api', configuration: 'testArtifacts')
     integrationImplementation project(path: ':iceberg-hive-metastore', configuration: 'testArtifacts')
     integrationImplementation(libs.flink21.test.utils) {
       exclude group: "org.apache.curator", module: 'curator-test'
-      exclude group: 'junit'
     }
 
+    integrationImplementation libs.flink21.connector.base
     integrationImplementation libs.flink21.table.api.java.bridge
     integrationImplementation "org.apache.flink:flink-table-planner_${scalaVersion}:${libs.versions.flink21.get()}"
 
@@ -226,7 +228,7 @@ project(":iceberg-flink:iceberg-flink-runtime-${flinkMajorVersion}") {
   shadowJar {
     configurations = [project.configurations.runtimeClasspath]
 
-    zip64 true
+    zip64 = true
 
     // include the LICENSE and NOTICE files for the shaded Jar
     from(projectDir) {
@@ -255,6 +257,9 @@ project(":iceberg-flink:iceberg-flink-runtime-${flinkMajorVersion}") {
   task integrationTest(type: Test) {
     description = "Test Flink Runtime Jar against Flink ${flinkMajorVersion}"
     group = "verification"
+    useJUnitPlatform {
+      excludeEngines "junit-vintage"
+    }
     jvmArgs += project.property('extraJvmArgs')
     testClassesDirs = sourceSets.integration.output.classesDirs
     classpath = sourceSets.integration.runtimeClasspath + files(shadowJar.archiveFile.get().asFile.path)
diff --git a/gcp-bundle/build.gradle b/gcp-bundle/build.gradle
index 6ebe05ccdbce..f2b048caa6ee 100644
--- a/gcp-bundle/build.gradle
+++ b/gcp-bundle/build.gradle
@@ -34,7 +34,7 @@ project(":iceberg-gcp-bundle") {
 
   shadowJar {
     archiveClassifier.set(null)
-    zip64 true
+    zip64 = true
 
     // include the LICENSE and NOTICE files for the shaded Jar
     from(projectDir) {
diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties
index 207c4600bb1b..41465649341d 100644
--- a/gradle/wrapper/gradle-wrapper.properties
+++ b/gradle/wrapper/gradle-wrapper.properties
@@ -1,7 +1,7 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionSha256Sum=f1771298a70f6db5a29daf62378c4e18a17fc33c9ba6b14362e0cdf40610380d
-distributionUrl=https\://services.gradle.org/distributions/gradle-8.14.4-bin.zip
+distributionSha256Sum=b266d5ff6b90eada6dc3b20cb090e3731302e553a27c5d3e4df1f0d76beaff06
+distributionUrl=https\://services.gradle.org/distributions/gradle-9.3.1-bin.zip
 networkTimeout=10000
 validateDistributionUrl=true
 zipStoreBase=GRADLE_USER_HOME
diff --git a/mr/build.gradle b/mr/build.gradle
index dac7e3d4542b..6efffae6546b 100644
--- a/mr/build.gradle
+++ b/mr/build.gradle
@@ -76,7 +76,7 @@ project(':iceberg-mr') {
 
   test {
     // testJoinTables / testScanTable
-    maxHeapSize '2500m'
+    maxHeapSize = '2500m'
   }
 }
 
diff --git a/spark/v3.4/build.gradle b/spark/v3.4/build.gradle
index 714ee703b842..adee7b926447 100644
--- a/spark/v3.4/build.gradle
+++ b/spark/v3.4/build.gradle
@@ -287,7 +287,7 @@ project(":iceberg-spark:iceberg-spark-runtime-${sparkMajorVersion}_${scalaVersio
   shadowJar {
     configurations = [project.configurations.runtimeClasspath]
 
-    zip64 true
+    zip64 = true
 
     // include the LICENSE and NOTICE files for the shaded Jar
     from(projectDir) {
diff --git a/spark/v3.5/build.gradle b/spark/v3.5/build.gradle
index 20a9cfb007bd..e95304382a76 100644
--- a/spark/v3.5/build.gradle
+++ b/spark/v3.5/build.gradle
@@ -289,7 +289,7 @@ project(":iceberg-spark:iceberg-spark-runtime-${sparkMajorVersion}_${scalaVersio
   shadowJar {
     configurations = [project.configurations.runtimeClasspath]
 
-    zip64 true
+    zip64 = true
 
     // include the LICENSE and NOTICE files for the shaded Jar
     from(projectDir) {
diff --git a/spark/v4.0/build.gradle b/spark/v4.0/build.gradle
index fb9df4e0e0f2..7274c5135942 100644
--- a/spark/v4.0/build.gradle
+++ b/spark/v4.0/build.gradle
@@ -132,7 +132,7 @@ project(":iceberg-spark:iceberg-spark-${sparkMajorVersion}_${scalaVersion}") {
 
   tasks.withType(Test) {
     // Vectorized reads need more memory
-    maxHeapSize '3160m'
+    maxHeapSize = '3160m'
   }
 }
 
@@ -298,7 +298,7 @@ project(":iceberg-spark:iceberg-spark-runtime-${sparkMajorVersion}_${scalaVersio
   shadowJar {
     configurations = [project.configurations.runtimeClasspath]
 
-    zip64 true
+    zip64 = true
 
     // include the LICENSE and NOTICE files for the shaded Jar
     from(projectDir) {
diff --git a/spark/v4.1/build.gradle b/spark/v4.1/build.gradle
index a342a0b59c92..f37eaf193819 100644
--- a/spark/v4.1/build.gradle
+++ b/spark/v4.1/build.gradle
@@ -133,7 +133,7 @@ project(":iceberg-spark:iceberg-spark-${sparkMajorVersion}_${scalaVersion}") {
 
   tasks.withType(Test) {
     // Vectorized reads need more memory
-    maxHeapSize '3160m'
+    maxHeapSize = '3160m'
   }
 }
 
@@ -300,7 +300,7 @@ project(":iceberg-spark:iceberg-spark-runtime-${sparkMajorVersion}_${scalaVersio
   shadowJar {
     configurations = [project.configurations.runtimeClasspath]
 
-    zip64 true
+    zip64 = true
 
     // include the LICENSE and NOTICE files for the shaded Jar
     from(projectDir) {
diff --git a/tasks.gradle b/tasks.gradle
index 5515d7b75052..42e7b30877bd 100644
--- a/tasks.gradle
+++ b/tasks.gradle
@@ -22,7 +22,7 @@ task aggregateJavadoc(type: Javadoc) {
   def javadocTasks = subprojects.findAll { it.name != 'iceberg-bom' }.javadoc
   dependsOn javadocTasks
   source javadocTasks.source
-  destinationDir project.rootProject.file("site/docs/javadoc/${getJavadocVersion()}")
+  destinationDir = project.rootProject.file("site/docs/javadoc/${getJavadocVersion()}")
   classpath = project.rootProject.files(javadocTasks.classpath)
 
   final JAVADOC_FIX_SEARCH_STR = '\n\n' +