diff --git a/scanner/src/main/kotlin/Scanner.kt b/scanner/src/main/kotlin/Scanner.kt
index f9ce8dc3a4c9d..d5a1b979d7fd1 100644
--- a/scanner/src/main/kotlin/Scanner.kt
+++ b/scanner/src/main/kotlin/Scanner.kt
@@ -356,15 +356,27 @@ class Scanner(
                     "Finished scan of ${nestedProvenance.root} with package scanner '${scanner.name}'."
                 }
 
+                val provenanceScanResultsToStore = mutableSetOf<Pair<KnownProvenance, ScanResult>>()
                 packagesWithIncompleteScanResult.forEach processResults@{ pkg ->
                     val nestedProvenanceScanResult = scanResult.toNestedProvenanceScanResult(nestedProvenance)
                     controller.addNestedScanResult(scanner, nestedProvenanceScanResult)
 
                     // TODO: Run in coroutine.
                     if (scanner.writeToStorage) {
-                        storeNestedScanResult(pkg, nestedProvenanceScanResult)
+                        storePackageScanResult(pkg, nestedProvenanceScanResult)
+
+                        nestedProvenanceScanResult.scanResults.forEach { (provenance, scanResults) ->
+                            scanResults.forEach { scanResult ->
+                                provenanceScanResultsToStore += provenance to scanResult
+                            }
+                        }
                     }
                 }
+
+                // Store only deduplicated provenance scan results.
+                provenanceScanResultsToStore.forEach { (provenance, scanResult) ->
+                    storeProvenanceScanResult(provenance, scanResult)
+                }
             }
         }
     }
@@ -601,16 +613,6 @@ class Scanner(
         }
     }
 
-    private fun storeNestedScanResult(pkg: Package, nestedProvenanceScanResult: NestedProvenanceScanResult) {
-        storePackageScanResult(pkg, nestedProvenanceScanResult)
-
-        nestedProvenanceScanResult.scanResults.forEach { (provenance, scanResults) ->
-            scanResults.forEach { scanResult ->
-                storeProvenanceScanResult(provenance, scanResult)
-            }
-        }
-    }
-
     private fun storeProvenanceScanResult(provenance: KnownProvenance, scanResult: ScanResult) {
         storageWriters.filterIsInstance<ProvenanceBasedScanStorageWriter>().forEach { writer ->
             runCatching {
diff --git a/scanner/src/test/kotlin/ScannerTest.kt b/scanner/src/test/kotlin/ScannerTest.kt
index 6b22bbbf50f43..5fade0e9c1adf 100644
--- a/scanner/src/test/kotlin/ScannerTest.kt
+++ b/scanner/src/test/kotlin/ScannerTest.kt
@@ -22,6 +22,7 @@ package org.ossreviewtoolkit.scanner
 import io.kotest.assertions.throwables.shouldThrow
 import io.kotest.core.spec.style.WordSpec
 import io.kotest.matchers.collections.beEmpty
+import io.kotest.matchers.collections.shouldContainExactly
 import io.kotest.matchers.maps.beEmpty as beEmptyMap
 import io.kotest.matchers.maps.containExactly
 import io.kotest.matchers.nulls.shouldNotBeNull
@@ -178,6 +179,35 @@ class ScannerTest : WordSpec({
 
             verify(exactly = 0) { provenanceDownloader.download(any()) }
         }
+
+        "store only a single scan result per provenance" {
+            val packageScanner = FakePackageScannerWrapper()
+
+            val pkgWithVcs1 = Package.new(name = "project1").withValidVcs()
+            val pkgWithVcs2 = Package.new(name = "project2").withValidVcs()
+            val pkgWithVcs3 = Package.new(name = "project3").withValidVcs()
+            val packageScannerResult = createScanResult(pkgWithVcs1.repositoryProvenance(), packageScanner.details)
+
+            val scannerWrapper = spyk(packageScanner) {
+                every { scanPackage(any(), any()) } returns packageScannerResult
+            }
+
+            val storedScanResults = mutableListOf<ScanResult>()
+            val writer = object : ProvenanceBasedScanStorageWriter {
+                override fun write(scanResult: ScanResult) {
+                    storedScanResults.add(scanResult)
+                }
+            }
+
+            val scanner = createScanner(
+                packageScannerWrappers = listOf(scannerWrapper),
+                storageWriters = listOf(writer)
+            )
+
+            scanner.scan(setOf(pkgWithVcs1, pkgWithVcs2, pkgWithVcs3), createContext())
+
+            storedScanResults shouldContainExactly listOf(packageScannerResult)
+        }
     }
 
     "Scanning with a provenance scanner" should {