diff --git a/plugins/hls-hlint-plugin/README.md b/plugins/hls-hlint-plugin/README.md
index fa775a35ca..77b33c0769 100644
--- a/plugins/hls-hlint-plugin/README.md
+++ b/plugins/hls-hlint-plugin/README.md
@@ -5,3 +5,9 @@
 This is typically done through an [HLint configuration file](https://github.com/ndmitchell/hlint#customizing-the-hints).
 You can also change the behavior of HLint by adding a list of flags to `haskell.plugin.hlint.config.flags`
 if your configuration is in a non-standard location or you want to change settings globally.
+
+## Known Differences from the `hlint` executable
+
+- The `hlint` executable by default turns on many extensions when parsing a file because it is not certain about the exact extensions that apply to the file (they may come from project files). This differs from HLS which uses only the extensions the file needs to parse the file. Hence it is possible for the `hlint` executable to report a parse error on a file, but the `hlint` plugin to work just fine on the same file. This does mean that the turning on/off of extensions in the hlint config may be ignored by the `hlint` plugin.
+- Hlint restrictions do not work (yet). This [PR](https://github.com/ndmitchell/hlint/pull/1340) should enable that functionality, but this requires a newer version of hlint to be used in HLS.
+
diff --git a/plugins/hls-hlint-plugin/src/Ide/Plugin/Hlint.hs b/plugins/hls-hlint-plugin/src/Ide/Plugin/Hlint.hs
index 7a73ccfb5b..7620003e33 100644
--- a/plugins/hls-hlint-plugin/src/Ide/Plugin/Hlint.hs
+++ b/plugins/hls-hlint-plugin/src/Ide/Plugin/Hlint.hs
@@ -55,7 +55,6 @@ import           Development.IDE.Core.Shake                         (getDiagnost
 import qualified Refact.Apply                                       as Refact
 
 #ifdef HLINT_ON_GHC_LIB
-import           Data.List                                          (nub)
 import           Development.IDE.GHC.Compat                         (BufSpan,
                                                                      DynFlags,
                                                                      WarningFlag (Opt_WarnUnrecognisedPragmas),
@@ -284,16 +283,26 @@ getIdeas nfp = do
                      Just <$> liftIO (parseModuleEx flags' fp contents')
 
         setExtensions flags = do
-          hlintExts <- getExtensions flags nfp
+          hlintExts <- getExtensions nfp
           debugm $ "hlint:getIdeas:setExtensions:" ++ show hlintExts
           return $ flags { enabledExtensions = hlintExts }
 
-getExtensions :: ParseFlags -> NormalizedFilePath -> Action [Extension]
-getExtensions pflags nfp = do
+-- Gets extensions from ModSummary dynflags for the file.
+-- Previously this would concatenate extensions from both hlint's parsedFlags
+-- and the ModSummary dynflags. However using the parsedFlags extensions
+-- can sometimes interfere with the hlint parsing of the file.
+-- See https://github.com/haskell/haskell-language-server/issues/1279
+--
+-- Note: this is used when HLINT_ON_GHC_LIB is not defined. We seem to need
+-- these extensions to construct dynflags to parse the file again. Therefore
+-- using hlint default extensions doesn't seem to be a problem when
+-- HLINT_ON_GHC_LIB is not defined because we don't parse the file again.
+getExtensions :: NormalizedFilePath -> Action [Extension]
+getExtensions nfp = do
     dflags <- getFlags
     let hscExts = EnumSet.toList (extensionFlags dflags)
     let hscExts' = mapMaybe (GhclibParserEx.readExtension . show) hscExts
-    let hlintExts = nub $ enabledExtensions pflags ++ hscExts'
+    let hlintExts = hscExts'
     return hlintExts
   where getFlags :: Action DynFlags
         getFlags = do
@@ -538,8 +547,7 @@ applyHint ide nfp mhint =
         liftIO $ withSystemTempFile (takeFileName fp) $ \temp h -> do
             hClose h
             writeFileUTF8NoNewLineTranslation temp oldContent
-            (pflags, _, _) <- runAction' $ useNoFile_ GetHlintSettings
-            exts <- runAction' $ getExtensions pflags nfp
+            exts <- runAction' $ getExtensions nfp
             -- We have to reparse extensions to remove the invalid ones
             let (enabled, disabled, _invalid) = Refact.parseExtensions $ map show exts
             let refactExts = map show $ enabled ++ disabled
diff --git a/plugins/hls-hlint-plugin/test/Main.hs b/plugins/hls-hlint-plugin/test/Main.hs
index 69d92a28dc..65242266c2 100644
--- a/plugins/hls-hlint-plugin/test/Main.hs
+++ b/plugins/hls-hlint-plugin/test/Main.hs
@@ -134,8 +134,7 @@ suggestionsTests =
         changeDoc doc [change']
         testHlintDiagnostics doc
 
-    , knownBrokenForHlintOnGhcLib "hlint doesn't take in account cpp flag as ghc -D argument" $
-      testCase "[#554] hlint diagnostics works with CPP via ghc -XCPP argument" $ runHlintSession "cpp" $ do
+    , testCase "[#554] hlint diagnostics works with CPP via ghc -XCPP argument" $ runHlintSession "cpp" $ do
         doc <- openDoc "CppCond.hs" "haskell"
         testHlintDiagnostics doc
 
@@ -212,8 +211,7 @@ suggestionsTests =
             length diags @?= 1
             unusedExt ^. L.code @?= Just (InR "refact:Unused LANGUAGE pragma")
 
-    , knownBrokenForHlintOnGhcLib "[#1279] hlint uses a fixed set of extensions" $
-      testCase "hlint should not activate extensions like PatternSynonyms" $ runHlintSession "" $ do
+    , testCase "[#1279] hlint should not activate extensions like PatternSynonyms" $ runHlintSession "" $ do
         doc <- openDoc "PatternKeyword.hs" "haskell"
 
         waitForAllProgressDone