diff --git a/CHANGELOG.md b/CHANGELOG.md
index cd0d605a..8e333f18 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,6 +9,10 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 ### Added
 * Added `.overrideToolchain` as a convenience for using a custom rust toolchain
 
+### Fixed
+* Fixed an issue where `mkDummySrc` would produce incorrect results for filtered
+  sources: #46
+
 ## [0.5.0] - 2022-06-12
 
 ### Changed
diff --git a/checks/mkDummySrcTests/default.nix b/checks/mkDummySrcTests/default.nix
index 21f632ab..a9bd9feb 100644
--- a/checks/mkDummySrcTests/default.nix
+++ b/checks/mkDummySrcTests/default.nix
@@ -1,22 +1,46 @@
-{ linkFarmFromDrvs
+{ lib
+, linkFarmFromDrvs
 , mkDummySrc
 , runCommand
 }:
 
 let
-  cmpDummySrc = name: path:
+  cmpDummySrcRaw = name: input: expected:
     let
       dummySrc = mkDummySrc {
-        src = path + "/input";
+        src = input;
       };
     in
     runCommand "compare-${name}" { } ''
-      diff -r ${path + /expected} ${dummySrc}
+      echo ${expected} ${dummySrc}
+      diff -r ${expected} ${dummySrc}
       touch $out
     '';
+
+  cmpDummySrc = name: path:
+    let
+      expected = path + "/expected";
+      input = path + "/input";
+
+      # Regression test for https://github.com/ipetkov/crane/issues/46
+      filteredInput = lib.cleanSourceWith {
+        src = input;
+        filter = path: type:
+          let baseName = builtins.baseNameOf path;
+          in
+          type == "directory" || lib.any (s: lib.hasPrefix s (builtins.baseNameOf path)) [
+            "Cargo"
+            "config"
+          ];
+      };
+    in
+    [
+      (cmpDummySrcRaw name input expected)
+      (cmpDummySrcRaw "${name}-filtered" filteredInput expected)
+    ];
 in
-linkFarmFromDrvs "cleanCargoToml" [
+linkFarmFromDrvs "cleanCargoToml" (lib.flatten [
   (cmpDummySrc "single" ./single)
   (cmpDummySrc "single-alt" ./single-alt)
   (cmpDummySrc "workspace" ./workspace)
-]
+])
diff --git a/lib/mkDummySrc.nix b/lib/mkDummySrc.nix
index d52ce868..1fdf630d 100644
--- a/lib/mkDummySrc.nix
+++ b/lib/mkDummySrc.nix
@@ -78,17 +78,25 @@ let
   # directory, we check if it happens to be an ancestor for an interesting file (i.e. is a prefix of
   # an interesting file). That way we are left with the smallest possible source needed for our
   # dummy derivation, and we bring any cache invalidation to a minimum. Whew!
-  mkBasePath = p: (toString p) + "/";
-  uncleanSrcBasePath = mkBasePath src;
 
-  uncleanFiles = findCargoFiles src;
+  # NB: if the `src` we were provided was filtered, make sure that we crawl the `origSrc`! Otherwise
+  # when we try to crawl the source Nix will evaluate the filter(s) fully resulting in a store path
+  # whose prefix won't match the paths we observe when we try to clean the source a bit further down
+  # (Nix optimizes multiple filters by running them all once against the original source).
+  # https://github.com/ipetkov/crane/issues/46
+  origSrc =
+    if src ? _isLibCleanSourceWith
+    then src.origSrc
+    else src;
+
+  uncleanSrcBasePath = (toString origSrc) + "/";
+  uncleanFiles = findCargoFiles origSrc;
 
   cargoTomlsBase = uncleanSrcBasePath;
   inherit (uncleanFiles) cargoTomls;
 
   cleanSrc =
     let
-      adjustPaths = builtins.map (p: removePrefix uncleanSrcBasePath (toString p));
       allUncleanFiles = map
         (p: removePrefix uncleanSrcBasePath (toString p))
         # Allow the default `Cargo.lock` location to be picked up here