diff --git a/plugins/reporters/evaluated-model/src/funTest/assets/evaluated-model-reporter-test-deduplicate-expected-output.yml b/plugins/reporters/evaluated-model/src/funTest/assets/evaluated-model-reporter-test-deduplicate-expected-output.yml
index d19012efff0da..f70d45594bfb6 100644
--- a/plugins/reporters/evaluated-model/src/funTest/assets/evaluated-model-reporter-test-deduplicate-expected-output.yml
+++ b/plugins/reporters/evaluated-model/src/funTest/assets/evaluated-model-reporter-test-deduplicate-expected-output.yml
@@ -8,6 +8,9 @@ path_excludes:
   pattern: "**/*.java"
   reason: "EXAMPLE_OF"
   comment: "These are example files."
+- _id: 2
+  pattern: "analyzer/src/funTest/assets/projects/synthetic/gradle/lib/excluded-file.dat"
+  reason: "DATA_FILE_OF"
 scope_excludes:
 - _id: 0
   pattern: "testCompile"
@@ -976,9 +979,7 @@ repository:
       paths:
       - 0
       - 1
-      - _id: 2
-        pattern: "analyzer/src/funTest/assets/projects/synthetic/gradle/lib/excluded-file.dat"
-        reason: "DATA_FILE_OF"
+      - 2
       scopes:
       - 0
     resolutions:
diff --git a/plugins/reporters/evaluated-model/src/funTest/assets/evaluated-model-reporter-test-expected-output.json b/plugins/reporters/evaluated-model/src/funTest/assets/evaluated-model-reporter-test-expected-output.json
index 3d43e0aca2164..df559f1740b35 100644
--- a/plugins/reporters/evaluated-model/src/funTest/assets/evaluated-model-reporter-test-expected-output.json
+++ b/plugins/reporters/evaluated-model/src/funTest/assets/evaluated-model-reporter-test-expected-output.json
@@ -9,6 +9,10 @@
     "pattern" : "**/*.java",
     "reason" : "EXAMPLE_OF",
     "comment" : "These are example files."
+  }, {
+    "_id" : 2,
+    "pattern" : "analyzer/src/funTest/assets/projects/synthetic/gradle/lib/excluded-file.dat",
+    "reason" : "DATA_FILE_OF"
   } ],
   "scope_excludes" : [ {
     "_id" : 0,
@@ -1073,11 +1077,7 @@
     },
     "config" : {
       "excludes" : {
-        "paths" : [ 0, 1, {
-          "_id" : 2,
-          "pattern" : "analyzer/src/funTest/assets/projects/synthetic/gradle/lib/excluded-file.dat",
-          "reason" : "DATA_FILE_OF"
-        } ],
+        "paths" : [ 0, 1, 2 ],
         "scopes" : [ 0 ]
       },
       "resolutions" : {
diff --git a/plugins/reporters/evaluated-model/src/funTest/assets/evaluated-model-reporter-test-expected-output.yml b/plugins/reporters/evaluated-model/src/funTest/assets/evaluated-model-reporter-test-expected-output.yml
index 67c85f2008fd8..8989432e8b14d 100644
--- a/plugins/reporters/evaluated-model/src/funTest/assets/evaluated-model-reporter-test-expected-output.yml
+++ b/plugins/reporters/evaluated-model/src/funTest/assets/evaluated-model-reporter-test-expected-output.yml
@@ -8,6 +8,9 @@ path_excludes:
   pattern: "**/*.java"
   reason: "EXAMPLE_OF"
   comment: "These are example files."
+- _id: 2
+  pattern: "analyzer/src/funTest/assets/projects/synthetic/gradle/lib/excluded-file.dat"
+  reason: "DATA_FILE_OF"
 scope_excludes:
 - _id: 0
   pattern: "testCompile"
@@ -980,9 +983,7 @@ repository:
       paths:
       - 0
       - 1
-      - _id: 2
-        pattern: "analyzer/src/funTest/assets/projects/synthetic/gradle/lib/excluded-file.dat"
-        reason: "DATA_FILE_OF"
+      - 2
       scopes:
       - 0
     resolutions:
diff --git a/plugins/reporters/evaluated-model/src/main/kotlin/EvaluatedModelMapper.kt b/plugins/reporters/evaluated-model/src/main/kotlin/EvaluatedModelMapper.kt
index f12c0d5539f82..7911b88ff3c32 100644
--- a/plugins/reporters/evaluated-model/src/main/kotlin/EvaluatedModelMapper.kt
+++ b/plugins/reporters/evaluated-model/src/main/kotlin/EvaluatedModelMapper.kt
@@ -147,7 +147,7 @@ internal class EvaluatedModelMapper(private val input: ReporterInput) {
             vulnerabilitiesResolutions = vulnerabilitiesResolutions,
             vulnerabilities = vulnerabilities,
             statistics = with(input) { getStatistics(ortResult, licenseInfoResolver, ortConfig) },
-            repository = input.ortResult.repository.deduplicateResolutions(),
+            repository = input.ortResult.repository.deduplicateResolutionsAndExcludes(),
             severeIssueThreshold = input.ortConfig.severeIssueThreshold,
             severeRuleViolationThreshold = input.ortConfig.severeRuleViolationThreshold,
             repositoryConfiguration = input.ortResult.repository.config.toYaml(),
@@ -724,23 +724,26 @@ internal class EvaluatedModelMapper(private val input: ReporterInput) {
         values.map { addIfRequired(it) }.distinct()
 
     /**
-     * Return a copy of the [RepositoryConfiguration] with [Resolutions] that refer to the same instances as the
-     * [ResolvedConfiguration] for equal [Resolutions]. This is required for the [EvaluatedModel] to contained indexed
-     * references instead of duplicate [Resolutions].
+     * Return a copy of the [RepositoryConfiguration] with [Resolutions] and [Excludes] that refer to the same instances
+     * as the [ResolvedConfiguration] for equal entries. This is required for the [EvaluatedModel] to contain indexed
+     * entries instead of duplicate ones.
      */
-    private fun Repository.deduplicateResolutions(): Repository {
+    private fun Repository.deduplicateResolutionsAndExcludes(): Repository {
         val resolutions = with(config.resolutions) {
             copy(
-                issues = issues.map { resolution -> issueResolutions.find { resolution == it } ?: resolution },
-                ruleViolations = ruleViolations.map { resolution ->
-                    ruleViolationResolutions.find { resolution == it } ?: resolution
-                },
-                vulnerabilities = vulnerabilities.map { resolution ->
-                    vulnerabilitiesResolutions.find { resolution == it } ?: resolution
-                }
+                issues = issues.map { issueResolutions.addIfRequired(it) },
+                ruleViolations = ruleViolations.map { ruleViolationResolutions.addIfRequired(it) },
+                vulnerabilities = vulnerabilities.map { vulnerabilitiesResolutions.addIfRequired(it) }
+            )
+        }
+
+        val excludes = with(config.excludes) {
+            copy(
+                paths = paths.map { pathExcludes.addIfRequired(it) },
+                scopes = scopes.map { scopeExcludes.addIfRequired(it) }
             )
         }
 
-        return copy(config = config.copy(resolutions = resolutions))
+        return copy(config = config.copy(excludes = excludes, resolutions = resolutions))
     }
 }