diff --git a/src/frontends/qt4/GuiDocument.cpp b/src/frontends/qt4/GuiDocument.cpp
index 8e47d9ed24..ec015597e9 100644
--- a/src/frontends/qt4/GuiDocument.cpp
+++ b/src/frontends/qt4/GuiDocument.cpp
@@ -1744,11 +1744,12 @@ void GuiDocument::applyView()
 	string const bibtex_command =
 		fromqstr(biblioModule->bibtexCO->itemData(
 			biblioModule->bibtexCO->currentIndex()).toString());
-	if (bibtex_command == "default")
+	string const bibtex_options =
+		fromqstr(biblioModule->bibtexOptionsED->text());
+	if (bibtex_command == "default" || bibtex_options.empty())
 		bp_.bibtex_command = bibtex_command;
 	else
-		bp_.bibtex_command = bibtex_command + " "
-			+ fromqstr(biblioModule->bibtexOptionsED->text());
+		bp_.bibtex_command = bibtex_command + " " + bibtex_options;
 
 	// Indices
 	indicesModule->apply(bp_);
diff --git a/src/frontends/qt4/GuiIndices.cpp b/src/frontends/qt4/GuiIndices.cpp
index d44a377d13..969b86ad5d 100644
--- a/src/frontends/qt4/GuiIndices.cpp
+++ b/src/frontends/qt4/GuiIndices.cpp
@@ -136,11 +136,11 @@ void GuiIndices::apply(BufferParams & params) const
 	string const index_command =
 		fromqstr(indexCO->itemData(
 			indexCO->currentIndex()).toString());
-	if (index_command == "default")
+	string const index_options = fromqstr(indexOptionsED->text());
+	if (index_command == "default" || index_options.empty())
 		params.index_command = index_command;
 	else
-		params.index_command = index_command + " "
-			+ fromqstr(indexOptionsED->text());
+		params.index_command = index_command + " " + index_options;
 }
 
 
diff --git a/src/frontends/qt4/GuiPrefs.cpp b/src/frontends/qt4/GuiPrefs.cpp
index 596233bdb8..818a3e2396 100644
--- a/src/frontends/qt4/GuiPrefs.cpp
+++ b/src/frontends/qt4/GuiPrefs.cpp
@@ -670,19 +670,29 @@ void PrefLatex::on_latexIndexCO_activated(int n)
 
 void PrefLatex::apply(LyXRC & rc) const
 {
+	// If bibtex is not empty, bibopt contains the options, otherwise
+	// it is a customized bibtex command with options.
 	QString const bibtex = latexBibtexCO->itemData(
 		latexBibtexCO->currentIndex()).toString();
+	QString const bibopt = latexBibtexED->text();
 	if (bibtex.isEmpty())
-		rc.bibtex_command = fromqstr(latexBibtexED->text());
+		rc.bibtex_command = fromqstr(bibopt);
+	else if (bibopt.isEmpty())
+		rc.bibtex_command = fromqstr(bibtex);
 	else
-		rc.bibtex_command = fromqstr(bibtex) + " " + fromqstr(latexBibtexED->text());
+		rc.bibtex_command = fromqstr(bibtex) + " " + fromqstr(bibopt);
 
+	// If index is not empty, idxopt contains the options, otherwise
+	// it is a customized index command with options.
 	QString const index = latexIndexCO->itemData(
 		latexIndexCO->currentIndex()).toString();
+	QString const idxopt = latexIndexED->text();
 	if (index.isEmpty())
-		rc.index_command = fromqstr(latexIndexED->text());
+		rc.index_command = fromqstr(idxopt);
+	else if (idxopt.isEmpty())
+		rc.index_command = fromqstr(index);
 	else
-		rc.index_command = fromqstr(index) + " " + fromqstr(latexIndexED->text());
+		rc.index_command = fromqstr(index) + " " + fromqstr(idxopt);
 
 	rc.fontenc = fromqstr(latexEncodingED->text());
 	rc.chktex_command = fromqstr(latexChecktexED->text());