diff --git a/src/App/Docs.hs b/src/App/Docs.hs
index 984f66a35..6dabe2696 100644
--- a/src/App/Docs.hs
+++ b/src/App/Docs.hs
@@ -1,6 +1,7 @@
 module App.Docs (
   userGuideUrl,
   newIssueUrl,
+  fossaYmlDocUrl,
 ) where
 
 import App.Version (versionNumber)
@@ -9,11 +10,14 @@ import Data.Text (Text)
 sourceCodeUrl :: Text
 sourceCodeUrl = "https://github.com/fossas/spectrometer"
 
+guidePathOf :: Text -> Text -> Text
+guidePathOf revision repoRelUrl = sourceCodeUrl <> "/blob/" <> revision <> repoRelUrl
+
 userGuideUrl :: Text
-userGuideUrl = guidePathOf $ maybe "master" ("v" <>) versionNumber
-  where
-    guidePathOf :: Text -> Text
-    guidePathOf revision = sourceCodeUrl <> "/blob/" <> revision <> "/docs/userguide.md"
+userGuideUrl = guidePathOf (maybe "master" ("v" <>) versionNumber) "/docs/userguide.md"
+
+fossaYmlDocUrl :: Text
+fossaYmlDocUrl = guidePathOf (maybe "master" ("v" <>) versionNumber) "/docs/reference/fossa_yml.md"
 
 newIssueUrl :: Text
 newIssueUrl = sourceCodeUrl <> "/issues/new"
diff --git a/src/App/Fossa/Configuration.hs b/src/App/Fossa/Configuration.hs
index fe75ae571..1a0f58e84 100644
--- a/src/App/Fossa/Configuration.hs
+++ b/src/App/Fossa/Configuration.hs
@@ -12,10 +12,15 @@ module App.Fossa.Configuration (
   ConfigPaths (..),
 ) where
 
+import App.Docs (fossaYmlDocUrl)
 import App.Types
 import Control.Carrier.Diagnostics qualified as Diag
+import Control.Effect.Lift (Lift)
 import Data.Aeson (FromJSON (parseJSON), withObject, (.!=), (.:), (.:?))
+import Data.Functor (($>))
 import Data.Text (Text)
+import Data.Text.Prettyprint.Doc (Doc, Pretty (pretty), vsep)
+import Effect.Logger (Severity (SevWarn), logWarn, withDefaultLogger)
 import Effect.ReadFS
 import Path
 import Path.IO (getCurrentDir)
@@ -103,7 +108,7 @@ instance FromJSON ConfigPaths where
 defaultFile :: Path Rel File
 defaultFile = $(mkRelFile ".fossa.yml")
 
-readConfigFile :: (Has ReadFS sig m, Has Diag.Diagnostics sig m) => Path Abs File -> m (Maybe ConfigFile)
+readConfigFile :: (Has (Lift IO) sig m, Has ReadFS sig m, Has Diag.Diagnostics sig m) => Path Abs File -> m (Maybe ConfigFile)
 readConfigFile file = do
   exists <- doesFileExist file
   if not exists
@@ -111,8 +116,18 @@ readConfigFile file = do
     else do
       readConfig <- readContentsYaml @ConfigFile file
       if configVersion readConfig < 3
-        then pure Nothing
+        then withDefaultLogger SevWarn (logWarn $ warnMsgForOlderConfig (configVersion readConfig)) $> Nothing
         else pure $ Just readConfig
+  where
+    warnMsgForOlderConfig :: Int -> Doc ann
+    warnMsgForOlderConfig foundVersion =
+      vsep
+        [ ""
+        , "Incompatible [.fossa.yml] found! Expecting `version: 3`; found `version: " <> pretty foundVersion <> "`"
+        , "Documentation for the new config file format can be found here:"
+        , "    " <> pretty fossaYmlDocUrl
+        , ""
+        ]
 
 readConfigFileIO :: IO (Maybe ConfigFile)
 readConfigFileIO = do
diff --git a/test/App/DocsSpec.hs b/test/App/DocsSpec.hs
index f635a1706..65d392a7b 100644
--- a/test/App/DocsSpec.hs
+++ b/test/App/DocsSpec.hs
@@ -2,7 +2,7 @@ module App.DocsSpec (
   spec,
 ) where
 
-import App.Docs (newIssueUrl, userGuideUrl)
+import App.Docs (fossaYmlDocUrl, newIssueUrl, userGuideUrl)
 import Data.Maybe (fromJust)
 import Data.Text (Text)
 import Network.HTTP.Req (
@@ -33,3 +33,7 @@ spec = do
   describe "newIssueUrl" $
     it "should be reachable" $
       newIssueUrl `shouldRespondToGETWithHttpCode` 200
+
+  describe "fossaYmlDocUrl" $
+    it "should be reachable" $
+      fossaYmlDocUrl `shouldRespondToGETWithHttpCode` 200
diff --git a/test/App/Fossa/Configuration/ConfigurationSpec.hs b/test/App/Fossa/Configuration/ConfigurationSpec.hs
index bb39fa03a..cb0a0138a 100644
--- a/test/App/Fossa/Configuration/ConfigurationSpec.hs
+++ b/test/App/Fossa/Configuration/ConfigurationSpec.hs
@@ -78,6 +78,9 @@ badFile = $(mkRelFile "test/App/Fossa/Configuration/testdata/invalidconfig.yml")
 missingFile :: Path Rel File
 missingFile = $(mkRelFile "test/App/Fossa/Configuration/testdata/missingfile.yml")
 
+ver2configFile :: Path Rel File
+ver2configFile = $(mkRelFile "test/App/Fossa/Configuration/testdata/ver2config.yml")
+
 spec :: T.Spec
 spec = do
   dir <- T.runIO getCurrentDir
@@ -85,6 +88,7 @@ spec = do
   config <- T.runIO . Diag.runDiagnostics $ runReadFSIO $ readConfigFile (dir </> testFile)
   badConfig <- T.runIO . Diag.runDiagnostics $ runReadFSIO $ readConfigFile (dir </> badFile)
   missingConfig <- T.runIO . Diag.runDiagnostics $ runReadFSIO $ readConfigFile (dir </> missingFile)
+  ver2Config <- T.runIO . Diag.runDiagnostics $ runReadFSIO $ readConfigFile (dir </> ver2configFile)
 
   T.describe "config file parser" $ do
     T.it "parses a full configuration file correctly" $
@@ -103,3 +107,8 @@ spec = do
       case missingConfig of
         Left _ -> T.expectationFailure "should have failed parsing"
         Right result -> result `T.shouldBe` Nothing
+
+    T.it "returns Nothing for incompatible file" $
+      case ver2Config of
+        Left err -> T.expectationFailure ("failed to parse config file" <> show (Diag.renderFailureBundle err))
+        Right result -> result `T.shouldBe` Nothing
diff --git a/test/App/Fossa/Configuration/testdata/ver2config.yml b/test/App/Fossa/Configuration/testdata/ver2config.yml
new file mode 100644
index 000000000..8f75b911e
--- /dev/null
+++ b/test/App/Fossa/Configuration/testdata/ver2config.yml
@@ -0,0 +1,16 @@
+
+   
+# Generated by FOSSA CLI (https://github.com/fossas/fossa-cli)
+# Visit https://fossa.com to learn more
+
+version: 2
+cli:
+  server: https://app.fossa.com
+  fetcher: custom
+  project: https://github.com/fossas/fossa-cli
+analyze:
+  modules:
+  - name: github.com/fossas/fossa-cli/cmd/fossa
+    type: go
+    target: github.com/fossas/fossa-cli/cmd/fossa
+    path: cmd/fossa
\ No newline at end of file