diff --git a/src/Text/Pandoc/App/CommandLineOptions.hs b/src/Text/Pandoc/App/CommandLineOptions.hs
index 4b9e691ed144..99dba4613485 100644
--- a/src/Text/Pandoc/App/CommandLineOptions.hs
+++ b/src/Text/Pandoc/App/CommandLineOptions.hs
@@ -283,21 +283,24 @@ options =
     , Option "H" ["include-in-header"]
                  (ReqArg
                   (\arg opt -> return opt{ optIncludeInHeader =
-                                             optIncludeInHeader opt ++ [arg] })
+                                             optIncludeInHeader opt ++
+                                             [normalizePath arg] })
                   "FILE")
                  "" -- "File to include at end of header (implies -s)"
 
     , Option "B" ["include-before-body"]
                  (ReqArg
                   (\arg opt -> return opt{ optIncludeBeforeBody =
-                                            optIncludeBeforeBody opt ++ [arg] })
+                                            optIncludeBeforeBody opt ++
+                                            [normalizePath arg] })
                   "FILE")
                  "" -- "File to include before document body"
 
     , Option "A" ["include-after-body"]
                  (ReqArg
                   (\arg opt -> return opt{ optIncludeAfterBody =
-                                            optIncludeAfterBody opt ++ [arg] })
+                                            optIncludeAfterBody opt ++
+                                            [normalizePath arg] })
                   "FILE")
                  "" -- "File to include after document body"
 
@@ -309,7 +312,8 @@ options =
     , Option "" ["highlight-style"]
                 (ReqArg
                  (\arg opt ->
-                     return opt{ optHighlightStyle = Just $ T.pack arg })
+                     return opt{ optHighlightStyle = Just $
+                                 T.pack $ normalizePath arg })
                  "STYLE|FILE")
                  "" -- "Style for highlighted code"
 
@@ -397,7 +401,7 @@ options =
     , Option "" ["reference-doc"]
                  (ReqArg
                   (\arg opt ->
-                    return opt { optReferenceDoc = Just arg })
+                    return opt { optReferenceDoc = Just $ normalizePath arg })
                   "FILE")
                  "" -- "Path of custom reference doc"
 
@@ -422,7 +426,8 @@ options =
 
     , Option "" ["abbreviations"]
                 (ReqArg
-                 (\arg opt -> return opt { optAbbreviations = Just arg })
+                 (\arg opt -> return opt { optAbbreviations =
+                                            Just $ normalizePath arg })
                 "FILE")
                 "" -- "Specify file for custom abbreviations"
 
@@ -607,21 +612,24 @@ options =
                  (ReqArg
                   (\arg opt ->
                      return opt { optVariables =
-                       setVariable "epub-cover-image" (T.pack arg) $
+                       setVariable "epub-cover-image"
+                         (T.pack $ normalizePath arg) $
                          optVariables opt })
                   "FILE")
                  "" -- "Path of epub cover image"
 
     , Option "" ["epub-metadata"]
                  (ReqArg
-                  (\arg opt -> return opt { optEpubMetadata = Just arg })
+                  (\arg opt -> return opt { optEpubMetadata = Just $
+                                             normalizePath arg })
                   "FILE")
                  "" -- "Path of epub metadata file"
 
     , Option "" ["epub-embed-font"]
                  (ReqArg
                   (\arg opt ->
-                     return opt{ optEpubFonts = arg : optEpubFonts opt })
+                     return opt{ optEpubFonts = normalizePath arg :
+                                                optEpubFonts opt })
                   "FILE")
                  "" -- "Directory of fonts to embed"
 
@@ -651,7 +659,8 @@ options =
     , Option "" ["bibliography"]
                  (ReqArg
                   (\arg opt -> return opt{ optMetadata =
-                                            addMeta "bibliography" arg $
+                                            addMeta "bibliography"
+                                              (normalizePath arg) $
                                               optMetadata opt })
                    "FILE")
                  ""
@@ -660,7 +669,8 @@ options =
                  (ReqArg
                   (\arg opt ->
                      return opt{ optMetadata =
-                                   addMeta "csl" arg $ optMetadata opt })
+                                   addMeta "csl" (normalizePath arg) $
+                                   optMetadata opt })
                    "FILE")
                  ""
 
@@ -668,8 +678,8 @@ options =
                  (ReqArg
                   (\arg opt ->
                      return opt{ optMetadata =
-                                  addMeta "citation-abbreviations" arg $
-                                    optMetadata opt })
+                                  addMeta "citation-abbreviations"
+                                    (normalizePath arg) $ optMetadata opt })
                    "FILE")
                  ""
 
@@ -752,7 +762,8 @@ options =
 
     , Option "" ["log"]
                  (ReqArg
-                  (\arg opt -> return opt{ optLogFile = Just arg })
+                  (\arg opt -> return opt{ optLogFile = Just $
+                                            normalizePath arg })
                 "FILE")
                 "" -- "Log messages in JSON format to this file."