diff --git a/Source/cmGlobalNinjaGenerator.cxx b/Source/cmGlobalNinjaGenerator.cxx
index c3989c046..8014c41b0 100644
--- a/Source/cmGlobalNinjaGenerator.cxx
+++ b/Source/cmGlobalNinjaGenerator.cxx
@@ -701,13 +701,22 @@ void cmGlobalNinjaGenerator::AddCXXCompileCommand(
     *this->CompileCommandsStream << "," << std::endl;
     }
 
+  std::string sourceFileName = sourceFile;
+  if (!cmSystemTools::FileIsFullPath(sourceFileName.c_str()))
+    {
+    sourceFileName = cmSystemTools::CollapseFullPath(
+      sourceFileName.c_str(),
+      this->GetCMakeInstance()->GetHomeOutputDirectory());
+    }
+
+
   *this->CompileCommandsStream << "\n{\n"
      << "  \"directory\": \""
      << cmGlobalGenerator::EscapeJSON(buildFileDir) << "\",\n"
      << "  \"command\": \""
      << cmGlobalGenerator::EscapeJSON(commandLine) << "\",\n"
      << "  \"file\": \""
-     << cmGlobalGenerator::EscapeJSON(sourceFile) << "\"\n"
+     << cmGlobalGenerator::EscapeJSON(sourceFileName) << "\"\n"
      << "}";
 }
 
diff --git a/Source/cmNinjaTargetGenerator.cxx b/Source/cmNinjaTargetGenerator.cxx
index 615793117..475898956 100644
--- a/Source/cmNinjaTargetGenerator.cxx
+++ b/Source/cmNinjaTargetGenerator.cxx
@@ -534,9 +534,21 @@ cmNinjaTargetGenerator
     cmLocalGenerator::RuleVariables compileObjectVars;
     std::string lang = language;
     compileObjectVars.Language = lang.c_str();
-    std::string escapedSourceFileName =
+
+    std::string escapedSourceFileName = sourceFileName;
+
+    if (!cmSystemTools::FileIsFullPath(sourceFileName.c_str()))
+      {
+      escapedSourceFileName = cmSystemTools::CollapseFullPath(
+        escapedSourceFileName.c_str(),
+        this->GetGlobalGenerator()->GetCMakeInstance()->
+          GetHomeOutputDirectory());
+      }
+
+    escapedSourceFileName =
       this->LocalGenerator->ConvertToOutputFormat(
-        sourceFileName.c_str(), cmLocalGenerator::SHELL);
+        escapedSourceFileName.c_str(), cmLocalGenerator::SHELL);
+
     compileObjectVars.Source = escapedSourceFileName.c_str();
     compileObjectVars.Object = objectFileName.c_str();
     compileObjectVars.Flags = vars["FLAGS"].c_str();