diff --git a/native-gradle-plugin/src/functionalTest/groovy/org/graalvm/buildtools/gradle/JavaApplicationFunctionalTest.groovy b/native-gradle-plugin/src/functionalTest/groovy/org/graalvm/buildtools/gradle/JavaApplicationFunctionalTest.groovy
index 028195c77..79b563b0c 100644
--- a/native-gradle-plugin/src/functionalTest/groovy/org/graalvm/buildtools/gradle/JavaApplicationFunctionalTest.groovy
+++ b/native-gradle-plugin/src/functionalTest/groovy/org/graalvm/buildtools/gradle/JavaApplicationFunctionalTest.groovy
@@ -227,8 +227,13 @@ class JavaApplicationFunctionalTest extends AbstractFunctionalTest {
         given:
         withSample("java-application")
         buildFile << """
-            graalvmNative.binaries.all {
-                verbose = true
+            graalvmNative {
+                useArgFile = false // required to check for --pgo flag
+                binaries {
+                    all {
+                        verbose = true
+                    }
+                }
             }
         """
 
diff --git a/native-gradle-plugin/src/functionalTest/groovy/org/graalvm/buildtools/gradle/NativeConfigRepoFunctionalTest.groovy b/native-gradle-plugin/src/functionalTest/groovy/org/graalvm/buildtools/gradle/NativeConfigRepoFunctionalTest.groovy
index 30d067106..1ab82dcc7 100644
--- a/native-gradle-plugin/src/functionalTest/groovy/org/graalvm/buildtools/gradle/NativeConfigRepoFunctionalTest.groovy
+++ b/native-gradle-plugin/src/functionalTest/groovy/org/graalvm/buildtools/gradle/NativeConfigRepoFunctionalTest.groovy
@@ -78,7 +78,7 @@ class NativeConfigRepoFunctionalTest extends AbstractFunctionalTest {
         outputContains "[graalvm reachability metadata repository for org.graalvm.internal:library-with-reflection:1.5]: Configuration directory not found. Trying latest version."
 
         and: "but finds one thanks to the latest configuration field"
-        outputContains "[graalvm reachability metadata repository for org.graalvm.internal:library-with-reflection:1.5]: Configuration directory is org.graalvm.internal/library-with-reflection/1"
+        outputContains "[graalvm reachability metadata repository for org.graalvm.internal:library-with-reflection:1.5]: Configuration directory is org.graalvm.internal" + File.separator + "library-with-reflection" + File.separator + "1"
 
         where:
         format   | label
diff --git a/native-gradle-plugin/src/functionalTest/groovy/org/graalvm/buildtools/gradle/OfficialMetadataRepoFunctionalTest.groovy b/native-gradle-plugin/src/functionalTest/groovy/org/graalvm/buildtools/gradle/OfficialMetadataRepoFunctionalTest.groovy
index 514af9793..57e3ad831 100644
--- a/native-gradle-plugin/src/functionalTest/groovy/org/graalvm/buildtools/gradle/OfficialMetadataRepoFunctionalTest.groovy
+++ b/native-gradle-plugin/src/functionalTest/groovy/org/graalvm/buildtools/gradle/OfficialMetadataRepoFunctionalTest.groovy
@@ -60,7 +60,7 @@ class OfficialMetadataRepoFunctionalTest extends AbstractFunctionalTest {
         }
 
         and: "finds metadata in the remote repository"
-        outputContains "[graalvm reachability metadata repository for com.h2database:h2:2.1.210]: Configuration directory is com.h2database/h2/2.1.210"
+        outputContains "[graalvm reachability metadata repository for com.h2database:h2:2.1.210]: Configuration directory is com.h2database" + File.separator + "h2" + File.separator + "2.1.210"
         outputDoesNotContain "Falling back to the default repository at"
     }
 
diff --git a/native-maven-plugin/src/functionalTest/groovy/org/graalvm/buildtools/maven/JavaApplicationFunctionalTest.groovy b/native-maven-plugin/src/functionalTest/groovy/org/graalvm/buildtools/maven/JavaApplicationFunctionalTest.groovy
index c49a29bb2..5509d88ae 100644
--- a/native-maven-plugin/src/functionalTest/groovy/org/graalvm/buildtools/maven/JavaApplicationFunctionalTest.groovy
+++ b/native-maven-plugin/src/functionalTest/groovy/org/graalvm/buildtools/maven/JavaApplicationFunctionalTest.groovy
@@ -43,6 +43,8 @@ package org.graalvm.buildtools.maven
 
 import spock.lang.Issue
 
+import static org.graalvm.buildtools.utils.SharedConstants.NATIVE_IMAGE_EXE;
+
 class JavaApplicationFunctionalTest extends AbstractGraalVMMavenFunctionalTest {
     def "proper options are added to the native-image invocation"() {
         withSample("java-application")
@@ -55,7 +57,9 @@ class JavaApplicationFunctionalTest extends AbstractGraalVMMavenFunctionalTest {
 
         then:
         buildSucceeded
-        outputContains "native-image -cp / -g --no-fallback --verbose --shared -Ob"
+        outputContains NATIVE_IMAGE_EXE
+        outputContains "-cp " // actual path is OS-specific (/ vs C:\)
+        outputContains "-g --no-fallback --verbose --shared -Ob"
     }
 
     def "can build and execute a native image with the Maven plugin"() {
@@ -116,7 +120,7 @@ class JavaApplicationFunctionalTest extends AbstractGraalVMMavenFunctionalTest {
 
         then:
         buildSucceeded
-        outputContains "Args file written to: target/native-image"
+        outputContains "Args file written to: target" + File.separator + "native-image"
     }
 
 }
diff --git a/native-maven-plugin/src/functionalTest/groovy/org/graalvm/buildtools/maven/MetadataRepositoryFunctionalTest.groovy b/native-maven-plugin/src/functionalTest/groovy/org/graalvm/buildtools/maven/MetadataRepositoryFunctionalTest.groovy
index 238a1e011..10c8ce04a 100644
--- a/native-maven-plugin/src/functionalTest/groovy/org/graalvm/buildtools/maven/MetadataRepositoryFunctionalTest.groovy
+++ b/native-maven-plugin/src/functionalTest/groovy/org/graalvm/buildtools/maven/MetadataRepositoryFunctionalTest.groovy
@@ -41,6 +41,8 @@
 
 package org.graalvm.buildtools.maven
 
+import static org.graalvm.buildtools.utils.SharedConstants.NATIVE_IMAGE_EXE;
+
 class MetadataRepositoryFunctionalTest extends AbstractGraalVMMavenFunctionalTest {
 
     void "if metadata is disabled, reflection fails"() {
@@ -70,7 +72,7 @@ class MetadataRepositoryFunctionalTest extends AbstractGraalVMMavenFunctionalTes
         outputContains "[graalvm reachability metadata repository for org.graalvm.internal:library-with-reflection:1.5]: Configuration directory not found. Trying latest version."
 
         and: "but it finds one thanks to the latest configuration field"
-        outputContains "[graalvm reachability metadata repository for org.graalvm.internal:library-with-reflection:1.5]: Configuration directory is org.graalvm.internal/library-with-reflection/1"
+        outputContains "[graalvm reachability metadata repository for org.graalvm.internal:library-with-reflection:1.5]: Configuration directory is org.graalvm.internal" + File.separator + "library-with-reflection" + File.separator + "1"
     }
 
     void "if excludeConfig is set it is added to the command line invocation"() {
@@ -82,7 +84,7 @@ class MetadataRepositoryFunctionalTest extends AbstractGraalVMMavenFunctionalTes
 
         then:
         buildSucceeded
-        outputContains "native-image --exclude-config dummy/path/to/file.jar \"*\""
+        outputContains NATIVE_IMAGE_EXE + " --exclude-config dummy/path/to/file.jar \"*\""
    }
 
     void "if the path doesn't exist it throws an error"() {
@@ -138,7 +140,7 @@ class MetadataRepositoryFunctionalTest extends AbstractGraalVMMavenFunctionalTes
         outputContains "[graalvm reachability metadata repository for org.graalvm.internal:library-with-reflection:1.5]: Configuration directory not found. Trying latest version."
 
         and: "but it finds one thanks to the latest configuration field"
-        outputContains "[graalvm reachability metadata repository for org.graalvm.internal:library-with-reflection:1.5]: Configuration directory is org.graalvm.internal/library-with-reflection/1"
+        outputContains "[graalvm reachability metadata repository for org.graalvm.internal:library-with-reflection:1.5]: Configuration directory is org.graalvm.internal" + File.separator + "library-with-reflection" + File.separator + "1"
     }
 
     void "it can download a remote repository"() {
@@ -158,7 +160,7 @@ class MetadataRepositoryFunctionalTest extends AbstractGraalVMMavenFunctionalTes
         outputContains "[graalvm reachability metadata repository for org.graalvm.internal:library-with-reflection:1.5]: Configuration directory not found. Trying latest version."
 
         and: "but it finds one thanks to the latest configuration field"
-        outputContains "[graalvm reachability metadata repository for org.graalvm.internal:library-with-reflection:1.5]: Configuration directory is org.graalvm.internal/library-with-reflection/1"
+        outputContains "[graalvm reachability metadata repository for org.graalvm.internal:library-with-reflection:1.5]: Configuration directory is org.graalvm.internal" + File.separator + "library-with-reflection" + File.separator + "1"
     }
 
     void "when pointing to a missing URL, reflection fails"() {
diff --git a/native-maven-plugin/src/functionalTest/groovy/org/graalvm/buildtools/maven/OfficialMetadataRepositoryFunctionalTest.groovy b/native-maven-plugin/src/functionalTest/groovy/org/graalvm/buildtools/maven/OfficialMetadataRepositoryFunctionalTest.groovy
index e78b2131c..7d0d18f7f 100644
--- a/native-maven-plugin/src/functionalTest/groovy/org/graalvm/buildtools/maven/OfficialMetadataRepositoryFunctionalTest.groovy
+++ b/native-maven-plugin/src/functionalTest/groovy/org/graalvm/buildtools/maven/OfficialMetadataRepositoryFunctionalTest.groovy
@@ -41,7 +41,10 @@
 
 package org.graalvm.buildtools.maven
 
+import spock.lang.IgnoreIf
+
 class OfficialMetadataRepositoryFunctionalTest extends AbstractGraalVMMavenFunctionalTest {
+    @IgnoreIf({ os.windows })
     void "the application runs when using the official metadata repository"() {
         given:
         withSample("metadata-repo-integration")
@@ -60,6 +63,7 @@ class OfficialMetadataRepositoryFunctionalTest extends AbstractGraalVMMavenFunct
         outputDoesNotContain "Falling back to the default repository."
     }
 
+    @IgnoreIf({ os.windows })
     void "the application runs when using the versioned official metadata repository"() {
         given:
         withSample("metadata-repo-integration")
diff --git a/samples/java-library/build.gradle b/samples/java-library/build.gradle
index b8eac6ff4..0b9c4d818 100644
--- a/samples/java-library/build.gradle
+++ b/samples/java-library/build.gradle
@@ -57,6 +57,7 @@ dependencies {
 }
 
 graalvmNative {
+    useArgFile = false // required to check for flags in tests
     binaries {
         main {
             verbose = true
diff --git a/samples/java-library/pom.xml b/samples/java-library/pom.xml
index 62ff4e893..778878e14 100644
--- a/samples/java-library/pom.xml
+++ b/samples/java-library/pom.xml
@@ -89,6 +89,7 @@
                             <imageName>${imageName}</imageName>
                             <fallback>false</fallback>
                             <sharedLibrary>true</sharedLibrary>
+                            <useArgFile>false</useArgFile>
                         </configuration>
                     </plugin>
                 </plugins>
diff --git a/samples/native-config-integration/pom.xml b/samples/native-config-integration/pom.xml
index 6d4729757..81ebfe939 100644
--- a/samples/native-config-integration/pom.xml
+++ b/samples/native-config-integration/pom.xml
@@ -94,6 +94,7 @@
                             <imageName>${imageName}</imageName>
                             <fallback>false</fallback>
                             <quickBuild>true</quickBuild>
+                            <useArgFile>false</useArgFile>
                         </configuration>
                     </plugin>
                 </plugins>