diff --git a/src/main/java/net/sf/jabref/model/database/BibDatabaseContext.java b/src/main/java/net/sf/jabref/model/database/BibDatabaseContext.java
index 8b54a4cf4e03..01603fcae6b9 100644
--- a/src/main/java/net/sf/jabref/model/database/BibDatabaseContext.java
+++ b/src/main/java/net/sf/jabref/model/database/BibDatabaseContext.java
@@ -191,11 +191,13 @@ public List<String> getFileDirectories(String fieldName, FileDirectoryPreference
         }
 
         // 3. preferences directory
-        preferences.getFileDirectory(fieldName).ifPresent(fileDirs::add);
+        preferences.getFileDirectory(fieldName).ifPresent(path ->
+            fileDirs.add(path.toAbsolutePath().toString())
+        );
 
         // 4. BIB file directory
-        getDatabaseFile().ifPresent(databaseFile -> {
-            String parentDir = databaseFile.getParent();
+        getDatabasePath().ifPresent(dbPath -> {
+            String parentDir = dbPath.getParent().toAbsolutePath().toString();
             // Check if we should add it as primary file dir (first in the list) or not:
             if (preferences.isBibLocationAsPrimary()) {
                 fileDirs.add(0, parentDir);
@@ -203,6 +205,7 @@ public List<String> getFileDirectories(String fieldName, FileDirectoryPreference
                 fileDirs.add(parentDir);
             }
         });
+
         return fileDirs;
     }
 
diff --git a/src/main/java/net/sf/jabref/model/metadata/FileDirectoryPreferences.java b/src/main/java/net/sf/jabref/model/metadata/FileDirectoryPreferences.java
index fb29d641ac03..1016911f8fc3 100644
--- a/src/main/java/net/sf/jabref/model/metadata/FileDirectoryPreferences.java
+++ b/src/main/java/net/sf/jabref/model/metadata/FileDirectoryPreferences.java
@@ -1,20 +1,21 @@
 package net.sf.jabref.model.metadata;
 
+import java.nio.file.InvalidPathException;
+import java.nio.file.Path;
+import java.nio.file.Paths;
 import java.util.Map;
 import java.util.Optional;
 
 import net.sf.jabref.model.entry.FieldName;
 
 public class FileDirectoryPreferences {
+    public static final String DIR_SUFFIX = "Directory";
 
     private final String user;
     private final Map<String, String> fieldFileDirectories;
     private final boolean bibLocationAsPrimary;
-    public static final String DIR_SUFFIX = "Directory";
-
 
-    public FileDirectoryPreferences(String user, Map<String, String> fieldFileDirectories,
-            boolean bibLocationAsPrimary) {
+    public FileDirectoryPreferences(String user, Map<String, String> fieldFileDirectories, boolean bibLocationAsPrimary) {
         this.user = user;
         this.fieldFileDirectories = fieldFileDirectories;
         this.bibLocationAsPrimary = bibLocationAsPrimary;
@@ -24,11 +25,21 @@ public String getUser() {
         return user;
     }
 
-    public Optional<String> getFileDirectory(String field) {
-        return Optional.ofNullable(fieldFileDirectories.get(field));
+    public Optional<Path> getFileDirectory(String field) {
+        try {
+            String value = fieldFileDirectories.get(field);
+            // filter empty paths
+            if (value != null && !value.isEmpty()) {
+                Path path = Paths.get(value);
+                return Optional.of(path);
+            }
+            return Optional.empty();
+        } catch(InvalidPathException ex) {
+            return Optional.empty();
+        }
     }
 
-    public Optional<String> getFileDirectory() {
+    public Optional<Path> getFileDirectory() {
         return getFileDirectory(FieldName.FILE);
     }