diff --git a/cli/application/src/main/java/com/buschmais/jqassistant/commandline/Main.java b/cli/application/src/main/java/com/buschmais/jqassistant/commandline/Main.java
index 5efe8701a..a8a205bcf 100644
--- a/cli/application/src/main/java/com/buschmais/jqassistant/commandline/Main.java
+++ b/cli/application/src/main/java/com/buschmais/jqassistant/commandline/Main.java
@@ -1,10 +1,7 @@
 package com.buschmais.jqassistant.commandline;
 
 import java.io.File;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Map;
-import java.util.Optional;
+import java.util.*;
 
 import com.buschmais.jqassistant.commandline.configuration.CliConfiguration;
 import com.buschmais.jqassistant.commandline.plugin.ArtifactProviderFactory;
@@ -52,6 +49,8 @@ public class Main {
 
     private static final String CMDLINE_OPTION_PROFILES = "-profiles";
 
+    private static final Set<String> IGNORE_PROPERTIES = Set.of("jqassistant.opts", "jqassistant.home"); //  env variables provided by jqassistant shell scripts
+
     /**
      * The main method.
      *
@@ -245,6 +244,7 @@ private CliConfiguration getCliConfiguration(CommandLine commandLine, File worki
             .withClasspath()
             .withEnvVariables()
             .withProfiles(profiles)
+            .withIgnoreProperties(IGNORE_PROPERTIES)
             .load(configSource, new SysPropConfigSource(), commandLineProperties, mavenSettingsConfigSource);
     }
 
diff --git a/core/runtime/src/main/java/com/buschmais/jqassistant/core/runtime/api/configuration/ConfigurationMappingLoader.java b/core/runtime/src/main/java/com/buschmais/jqassistant/core/runtime/api/configuration/ConfigurationMappingLoader.java
index 4417fe248..322fa0f1d 100644
--- a/core/runtime/src/main/java/com/buschmais/jqassistant/core/runtime/api/configuration/ConfigurationMappingLoader.java
+++ b/core/runtime/src/main/java/com/buschmais/jqassistant/core/runtime/api/configuration/ConfigurationMappingLoader.java
@@ -9,10 +9,7 @@
 import java.nio.file.Paths;
 import java.nio.file.SimpleFileVisitor;
 import java.nio.file.attribute.BasicFileAttributes;
-import java.util.ArrayList;
-import java.util.Enumeration;
-import java.util.List;
-import java.util.Map;
+import java.util.*;
 
 import io.smallrye.config.*;
 import io.smallrye.config.source.yaml.YamlConfigSource;
@@ -96,6 +93,8 @@ public static class Builder<C extends Configuration> {
 
         private final List<String> profiles = new ArrayList<>();
 
+        private final Set<String> ignoreProperties = new HashSet<>();
+
         private Builder(Class<C> configurationMapping, List<String> configLocations) {
             this.configurationMapping = configurationMapping;
             if (configLocations.isEmpty()) {
@@ -183,6 +182,18 @@ public Builder<C> withProfiles(List<String> profiles) {
             return this;
         }
 
+        /**
+         * Add properties to ignore.
+         *
+         * @param ignoreProperties
+         *     The properties to ignore.
+         * @return The {@link Builder}.
+         */
+        public Builder<C> withIgnoreProperties(Collection<String> ignoreProperties) {
+            this.ignoreProperties.addAll(ignoreProperties);
+            return this;
+        }
+
         /**
          * Load the {@link Configuration} using the given directory including
          * <p/>
@@ -205,9 +216,10 @@ public C load(ConfigSource... additionalConfigSources) {
             // Create final config including validation, including only jqassistant properties
             Map<String, String> interpolatedProperties = stream(interpolatedConfig.getPropertyNames()
                 .spliterator(), false).filter(property -> property.startsWith(Configuration.PREFIX))
+                .filter(property -> !ignoreProperties.contains(property))
                 .collect(toMap(property -> property, interpolatedConfig::getRawValue));
             SmallRyeConfig config = new SmallRyeConfigBuilder().withMapping(configurationMapping)
-                .withSources(new PropertiesConfigSource(interpolatedProperties, "Interpolated Configuration", ConfigSource.DEFAULT_ORDINAL))
+                .withSources(new PropertiesConfigSource(interpolatedProperties, "jQAssistant Configuration", ConfigSource.DEFAULT_ORDINAL))
                 .build();
             C configMapping = config.getConfigMapping(configurationMapping);
             if (log.isDebugEnabled()) {
diff --git a/core/runtime/src/test/java/com/buschmais/jqassistant/core/runtime/impl/configuration/ConfigurationMappingLoaderTest.java b/core/runtime/src/test/java/com/buschmais/jqassistant/core/runtime/impl/configuration/ConfigurationMappingLoaderTest.java
index 22e959360..ff50bd1ae 100644
--- a/core/runtime/src/test/java/com/buschmais/jqassistant/core/runtime/impl/configuration/ConfigurationMappingLoaderTest.java
+++ b/core/runtime/src/test/java/com/buschmais/jqassistant/core/runtime/impl/configuration/ConfigurationMappingLoaderTest.java
@@ -3,6 +3,7 @@
 import java.io.File;
 import java.util.List;
 import java.util.Map;
+import java.util.Set;
 
 import com.buschmais.jqassistant.core.runtime.api.configuration.ConfigurationMappingLoader;
 import com.buschmais.jqassistant.core.scanner.api.configuration.Scan;
@@ -94,6 +95,19 @@ void unknownProperty() {
             .withMessageContaining(unknownProperty);
     }
 
+    @Test
+    void ignoreProperty() {
+        String unknownProperty = "jqassistant.unknown";
+
+        TestConfiguration configuration = ConfigurationMappingLoader.builder(TestConfiguration.class, emptyList())
+            .withUserHome(USER_HOME)
+            .withWorkingDirectory(WORKING_DIRECTORY)
+            .withIgnoreProperties(Set.of(unknownProperty))
+            .load(new PropertiesConfigSource(Map.of(unknownProperty, "test value"), "Test", ConfigSource.DEFAULT_ORDINAL));
+
+        assertThat(configuration).isNotNull();
+    }
+
     @Test
     @SetEnvironmentVariable(key = "jqassistant_scan_continue_on_error", value = "false")
     void overrideFromEnvVariable() {