diff --git a/plugins/org.python.pydev.ast/src/org/python/pydev/ast/interpreter_managers/DefaultPathsForInterpreterInfo.java b/plugins/org.python.pydev.ast/src/org/python/pydev/ast/interpreter_managers/DefaultPathsForInterpreterInfo.java
index c47d6158e0..567f6743ff 100644
--- a/plugins/org.python.pydev.ast/src/org/python/pydev/ast/interpreter_managers/DefaultPathsForInterpreterInfo.java
+++ b/plugins/org.python.pydev.ast/src/org/python/pydev/ast/interpreter_managers/DefaultPathsForInterpreterInfo.java
@@ -45,6 +45,10 @@ public boolean selectByDefault(String data) {
         return !isChildOfRootPath(data, rootPaths);
     }
 
+    public boolean forceDeselect(String data) {
+        return isRootPath(data, rootPaths);
+    }
+
     public boolean exists(String data) {
         return new File(data).exists();
     }
@@ -74,6 +78,21 @@ public static boolean isChildOfRootPath(String data, Set<IPath> rootPaths) {
         return false;
     }
 
+    public static boolean isRootPath(String data, Set<IPath> rootPaths) {
+        java.nio.file.Path nativePath = new File(data).toPath();
+
+        for (IPath p : rootPaths) {
+            try {
+                if (Files.isSameFile(nativePath, p.toFile().toPath())) {
+                    return true;
+                }
+            } catch (IOException e) {
+                Log.log(e);
+            }
+        }
+        return false;
+    }
+
     /**
      * Creates a Set of the root paths of all projects (and the workspace root itself).
      * @return A HashSet of root paths.
diff --git a/plugins/org.python.pydev.ast/src/org/python/pydev/ast/interpreter_managers/InterpreterInfo.java b/plugins/org.python.pydev.ast/src/org/python/pydev/ast/interpreter_managers/InterpreterInfo.java
index 44bf3e7996..6283a270a5 100644
--- a/plugins/org.python.pydev.ast/src/org/python/pydev/ast/interpreter_managers/InterpreterInfo.java
+++ b/plugins/org.python.pydev.ast/src/org/python/pydev/ast/interpreter_managers/InterpreterInfo.java
@@ -35,6 +35,7 @@
 
 import org.eclipse.core.runtime.Assert;
 import org.eclipse.core.runtime.CoreException;
+import org.eclipse.core.runtime.IPath;
 import org.eclipse.core.runtime.IProgressMonitor;
 import org.eclipse.core.runtime.Path;
 import org.eclipse.core.runtime.SafeRunner;
@@ -375,6 +376,8 @@ public static InterpreterInfo fromString(String received, boolean askUserInOutPa
                     DefaultPathsForInterpreterInfo defaultPaths = new DefaultPathsForInterpreterInfo(
                             resolvingInterpreter);
 
+                    Set<IPath> pythonHomePaths = new HashSet<>();
+
                     for (int j = 0; j < xmlNodes.getLength(); j++) {
                         Node xmlChild = xmlNodes.item(j);
                         String name = xmlChild.getNodeName();
@@ -388,6 +391,14 @@ public static InterpreterInfo fromString(String received, boolean askUserInOutPa
                         } else if ("executable".equals(name)) {
                             infoExecutable = data;
 
+                            // Handling of python inside of project.
+                            File pythonExecutableFile = new File(infoExecutable);
+                            File pythonHome = pythonExecutableFile.getParentFile();
+                            if (new File(pythonHome, "pyenv.cfg").exists()) {
+                                pythonHome = pythonHome.getParentFile();
+                            }
+                            pythonHomePaths.add(Path.fromOSString(pythonHome.toString()));
+
                         } else if ("vmArgs".equals(name)) {
                             infoVmArgs = data;
 
@@ -410,10 +421,17 @@ public static InterpreterInfo fromString(String received, boolean askUserInOutPa
                                     if (askUserInOutPath) {
                                         toAsk.add(data);
                                     }
-                                    //Select only if path is not child of a root path
-                                    if (defaultPaths.selectByDefault(data)) {
-                                        selection.add(data);
+
+                                    if (!defaultPaths.forceDeselect(data)) { // It's directly a project source folder (don't add it).
+                                        // If it's site-package, in python home or not under a source folder add it.
+                                        if (data.contains("site-packages")
+                                                || (DefaultPathsForInterpreterInfo
+                                                        .isChildOfRootPath(data, pythonHomePaths))
+                                                || defaultPaths.selectByDefault(data)) {
+                                            selection.add(data);
+                                        }
                                     }
+
                                 }
 
                             } else {