diff --git a/CHANGELOG.md b/CHANGELOG.md
index 331c0d41e44..d2537c6b3a5 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -43,6 +43,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 
 ### Fixed
 
+- We fixed to only search file links in the BIB file location directory when preferences has corresponding checkbox checked. [#5891](https://github.com/JabRef/jabref/issues/5891)
 - We fixed wrong button order (Apply and Cancel) in ManageProtectedTermsDialog.
 - We fixed an issue with incompatible characters at BibTeX key [#6257](https://github.com/JabRef/jabref/issues/6257)
 - We fixed an issue where dash (`-`) was reported as illegal BibTeX key [#6295](https://github.com/JabRef/jabref/issues/6295)
diff --git a/src/main/java/org/jabref/gui/preferences/FileTab.fxml b/src/main/java/org/jabref/gui/preferences/FileTab.fxml
index dd1f0d4c949..ccc58a72841 100644
--- a/src/main/java/org/jabref/gui/preferences/FileTab.fxml
+++ b/src/main/java/org/jabref/gui/preferences/FileTab.fxml
@@ -43,7 +43,7 @@
         <TextField fx:id="mainFileDir" HBox.hgrow="ALWAYS"/>
         <Button onAction="#mainFileDirBrowse" text="%Browse"/>
     </HBox>
-    <CheckBox fx:id="useBibLocationAsPrimary" text="%Use the BIB file location as primary file directory">
+    <CheckBox fx:id="useBibLocationAsPrimary" text="%Search and store files relative to library file location">
         <tooltip>
             <Tooltip
                     text="%When downloading files, or moving linked files to the file directory, prefer the BIB file location rather than the file directory set above"/>
diff --git a/src/main/java/org/jabref/model/database/BibDatabaseContext.java b/src/main/java/org/jabref/model/database/BibDatabaseContext.java
index f6f56dc5bd7..20d3c85ddbb 100644
--- a/src/main/java/org/jabref/model/database/BibDatabaseContext.java
+++ b/src/main/java/org/jabref/model/database/BibDatabaseContext.java
@@ -144,8 +144,6 @@ public List<Path> getFileDirectoriesAsPaths(FilePreferences preferences) {
             // Check if we should add it as primary file dir (first in the list) or not:
             if (preferences.isBibLocationAsPrimary()) {
                 fileDirs.add(0, parentPath);
-            } else {
-                fileDirs.add(parentPath);
             }
         });
 
diff --git a/src/main/resources/l10n/JabRef_en.properties b/src/main/resources/l10n/JabRef_en.properties
index 16466cd3606..3f804c858d4 100644
--- a/src/main/resources/l10n/JabRef_en.properties
+++ b/src/main/resources/l10n/JabRef_en.properties
@@ -1096,7 +1096,7 @@ Web\ search=Web search
 Style\ selection=Style selection
 No\ valid\ style\ file\ defined=No valid style file defined
 Choose\ pattern=Choose pattern
-Use\ the\ BIB\ file\ location\ as\ primary\ file\ directory=Use the BIB file location as primary file directory
+Search\ and\ store\ files\ relative\ to\ library\ file\ location=Search and store files relative to library file location
 Could\ not\ run\ the\ gnuclient/emacsclient\ program.\ Make\ sure\ you\ have\ the\ emacsclient/gnuclient\ program\ installed\ and\ available\ in\ the\ PATH.=Could not run the gnuclient/emacsclient program. Make sure you have the emacsclient/gnuclient program installed and available in the PATH.
 You\ must\ select\ either\ a\ valid\ style\ file,\ or\ use\ one\ of\ the\ default\ styles.=You must select either a valid style file, or use one of the default styles.
 
diff --git a/src/main/resources/l10n/JabRef_ru.properties b/src/main/resources/l10n/JabRef_ru.properties
index 563b20b2f5e..a549310e395 100644
--- a/src/main/resources/l10n/JabRef_ru.properties
+++ b/src/main/resources/l10n/JabRef_ru.properties
@@ -2168,7 +2168,7 @@ This\ entry\ type\ is\ intended\ for\ sources\ such\ as\ web\ sites\ which\ are\
 A\ single-volume\ work\ of\ reference\ such\ as\ an\ encyclopedia\ or\ a\ dictionary.=Неделимая работа или ссылка, как энциклопедия или словарь.
 A\ technical\ report,\ research\ report,\ or\ white\ paper\ published\ by\ a\ university\ or\ some\ other\ institution.=Технический отчет, исследовательский отчет, или белая книга, выпущенная институтом или другим учреждением.
 An\ entry\ set\ is\ a\ group\ of\ entries\ which\ are\ cited\ as\ a\ single\ reference\ and\ listed\ as\ a\ single\ item\ in\ the\ bibliography.=Набор записей представляет собой группу записей, которые приводятся в виде единой ссылки и перечислены в виде одного элемента в библиографии.
-Supplemental\ material\ in\ a\ "Book".\ This\ type\ is\ provided\ for\ elements\ such\ as\ prefaces,\ introductions,\ forewords,\ afterwords,\ etc.\ which\ often\ have\ a\ generic\ title\ only.=Дополнительный материал в "Книге" предназначен для таких элементов, как предисловия, введения, послесловия и т.д. 
+Supplemental\ material\ in\ a\ "Book".\ This\ type\ is\ provided\ for\ elements\ such\ as\ prefaces,\ introductions,\ forewords,\ afterwords,\ etc.\ which\ often\ have\ a\ generic\ title\ only.=Дополнительный материал в "Книге" предназначен для таких элементов, как предисловия, введения, послесловия и т.д.
 Supplemental\ material\ in\ a\ "Collection".=Дополнительные материалы в "Коллекции".
 Supplemental\ material\ in\ a\ "Periodical".\ This\ type\ may\ be\ useful\ when\ referring\ to\ items\ such\ as\ regular\ columns,\ obituaries,\ letters\ to\ the\ editor,\ etc.\ which\ only\ have\ a\ generic\ title.=Дополнительные материалы в "Периодическом издании". Этот тип может быть полезен при обращении к таким элементам, как обычные колонки, некрологи, письма к редактору и т.д., которые имеют только общее название.
 A\ thesis\ written\ for\ an\ educational\ institution\ to\ satisfy\ the\ requirements\ for\ a\ degree.=Тезис, написанный для учебного заведения с целью удовлетворения требований к степени.
diff --git a/src/test/java/org/jabref/gui/externalfiles/AutoSetFileLinksUtilTest.java b/src/test/java/org/jabref/gui/externalfiles/AutoSetFileLinksUtilTest.java
index 1bcd3895338..a56080661ed 100644
--- a/src/test/java/org/jabref/gui/externalfiles/AutoSetFileLinksUtilTest.java
+++ b/src/test/java/org/jabref/gui/externalfiles/AutoSetFileLinksUtilTest.java
@@ -30,24 +30,31 @@ public class AutoSetFileLinksUtilTest {
     private final BibDatabaseContext databaseContext = mock(BibDatabaseContext.class);
     private final ExternalFileTypes externalFileTypes = mock(ExternalFileTypes.class);
     private final BibEntry entry = new BibEntry(StandardEntryType.Article);
+    private Path path = null;
 
     @BeforeEach
     public void setUp(@TempDir Path folder) throws Exception {
-        Path path = folder.resolve("CiteKey.pdf");
+        path = folder.resolve("CiteKey.pdf");
         Files.createFile(path);
         entry.setCiteKey("CiteKey");
-        when(databaseContext.getFileDirectoriesAsPaths(any())).thenReturn(Collections.singletonList(path.getParent()));
         when(externalFileTypes.getExternalFileTypeSelection()).thenReturn(new TreeSet<>(ExternalFileTypes.getDefaultExternalFileTypes()));
     }
 
     @Test
-    public void test() throws Exception {
+    public void testFindAssociatedNotLinkedFilesSuccess() throws Exception {
         // Due to mocking the externalFileType class, the file extension will not be found
-
+        when(databaseContext.getFileDirectoriesAsPaths(any())).thenReturn(Collections.singletonList(path.getParent()));
         List<LinkedFile> expected = Collections.singletonList(new LinkedFile("", "CiteKey.pdf", ""));
-
         AutoSetFileLinksUtil util = new AutoSetFileLinksUtil(databaseContext, fileDirPrefs, autoLinkPrefs, externalFileTypes);
         List<LinkedFile> actual = util.findAssociatedNotLinkedFiles(entry);
         assertEquals(expected, actual);
     }
+
+    @Test
+    public void testFindAssociatedNotLinkedFilesForEmptySearchDir() throws Exception {
+        when(fileDirPrefs.isBibLocationAsPrimary()).thenReturn(false);
+        AutoSetFileLinksUtil util = new AutoSetFileLinksUtil(databaseContext, fileDirPrefs, autoLinkPrefs, externalFileTypes);
+        List<LinkedFile> actual = util.findAssociatedNotLinkedFiles(entry);
+        assertEquals(Collections.emptyList(), actual);
+    }
 }
diff --git a/src/test/java/org/jabref/logic/cleanup/MoveFilesCleanupTest.java b/src/test/java/org/jabref/logic/cleanup/MoveFilesCleanupTest.java
index 22ef8bd86e7..a237f03d6d8 100644
--- a/src/test/java/org/jabref/logic/cleanup/MoveFilesCleanupTest.java
+++ b/src/test/java/org/jabref/logic/cleanup/MoveFilesCleanupTest.java
@@ -4,8 +4,11 @@
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.util.Arrays;
+import java.util.Collections;
+import java.util.List;
 import java.util.Optional;
 
+import org.jabref.model.FieldChange;
 import org.jabref.model.database.BibDatabase;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
@@ -32,6 +35,7 @@ class MoveFilesCleanupTest {
     private MoveFilesCleanup cleanup;
     private BibEntry entry;
     private FilePreferences filePreferences;
+    private BibDatabaseContext databaseContext;
 
     @BeforeEach
     void setUp(@TempDir Path bibFolder) throws IOException {
@@ -47,7 +51,7 @@ void setUp(@TempDir Path bibFolder) throws IOException {
 
         MetaData metaData = new MetaData();
         metaData.setDefaultFileDirectory(defaultFileFolder.toAbsolutePath().toString());
-        BibDatabaseContext databaseContext = new BibDatabaseContext(new BibDatabase(), metaData);
+        databaseContext = new BibDatabaseContext(new BibDatabase(), metaData);
         Files.createFile(bibFolder.resolve("test.bib"));
         databaseContext.setDatabasePath(bibFolder.resolve("test.bib"));
 
@@ -119,4 +123,12 @@ void movesFileWithSubdirectoryPattern() throws Exception {
         assertFalse(Files.exists(fileBefore));
         assertTrue(Files.exists(fileAfter));
     }
+
+    @Test
+    void movesFileWithNoDirectory() throws Exception {
+        databaseContext.setMetaData(new MetaData());
+        when(filePreferences.getFileDirPattern()).thenReturn("");
+        List<FieldChange> changes = cleanup.cleanup(entry);
+        assertEquals(Collections.emptyList(), changes);
+    }
 }
diff --git a/src/test/java/org/jabref/logic/integrity/IntegrityCheckTest.java b/src/test/java/org/jabref/logic/integrity/IntegrityCheckTest.java
index 1401fcf08b9..aa7b3fa5723 100644
--- a/src/test/java/org/jabref/logic/integrity/IntegrityCheckTest.java
+++ b/src/test/java/org/jabref/logic/integrity/IntegrityCheckTest.java
@@ -36,6 +36,7 @@
 import static org.junit.jupiter.api.Assertions.assertNotEquals;
 import static org.mockito.ArgumentMatchers.any;
 import static org.mockito.Mockito.mock;
+import static org.mockito.Mockito.when;
 
 /**
  * This class tests the Integrity Checker as a whole.
@@ -177,8 +178,10 @@ private void assertWrong(BibDatabaseContext context) {
     }
 
     private void assertCorrect(BibDatabaseContext context) {
+        FilePreferences filePreferencesMock = mock(FilePreferences.class);
+        when(filePreferencesMock.isBibLocationAsPrimary()).thenReturn(true);
         List<IntegrityMessage> messages = new IntegrityCheck(context,
-                mock(FilePreferences.class),
+                filePreferencesMock,
                 createBibtexKeyPatternPreferences(),
                 JournalAbbreviationLoader.loadBuiltInRepository(), false
         ).check();