diff --git a/.github/workflows/eval.yml b/.github/workflows/eval.yml
index 6f86d8587200..2d22270c4874 100644
--- a/.github/workflows/eval.yml
+++ b/.github/workflows/eval.yml
@@ -135,12 +135,23 @@ jobs:
           github-token: ${{ github.token }}
           merge-multiple: true
 
-      - name: Upload the output paths and eval stats
+      - name: Compare outpaths against the target branch
+        if: steps.targetRunId.outputs.targetRunId
+        env:
+          MATRIX_SYSTEM: ${{ matrix.system }}
+        run: |
+          nix-build untrusted/ci -A eval.diff \
+            --arg beforeDir ./target \
+            --arg afterDir "$(readlink ./merged)" \
+            --argstr evalSystem "$MATRIX_SYSTEM" \
+            --out-link diff
+
+      - name: Upload outpaths diff and stats
         if: steps.targetRunId.outputs.targetRunId
         uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4.6.2
         with:
-          name: target-${{ matrix.system }}
-          path: target/*
+          name: diff-${{ matrix.system }}
+          path: diff/*
 
   process:
     name: Process
@@ -148,18 +159,11 @@ jobs:
     needs: [ prepare, outpaths ]
     if: needs.prepare.outputs.targetSha
     steps:
-      - name: Download output paths and eval stats for all systems (PR)
+      - name: Download output paths and eval stats for all systems
         uses: actions/download-artifact@fa0a91b85d4f404e444e00e005971372dc801d16 # v4.1.8
         with:
-          pattern: merged-*
-          path: merged
-          merge-multiple: true
-
-      - name: Download output paths and eval stats for all systems (target)
-        uses: actions/download-artifact@fa0a91b85d4f404e444e00e005971372dc801d16 # v4.1.8
-        with:
-          pattern: target-*
-          path: target
+          pattern: diff-*
+          path: diff
           merge-multiple: true
 
       - name: Check out the PR at the target commit
@@ -173,18 +177,11 @@ jobs:
         with:
           extra_nix_config: sandbox = true
 
-      - name: Combine all output paths and eval stats (PR)
+      - name: Combine all output paths and eval stats
         run: |
           nix-build trusted/ci -A eval.combine \
-            --arg evalDir ./merged \
-            --out-link combinedMerged
-
-      - name: Combine all output paths and eval stats (target)
-        if: needs.prepare.outputs.targetSha
-        run: |
-          nix-build trusted/ci -A eval.combine \
-            --arg evalDir ./target \
-            -o combinedTarget
+            --arg diffDir ./diff \
+            --out-link combined
 
       - name: Compare against the target branch
         env:
@@ -196,8 +193,7 @@ jobs:
 
           # Use the target branch to get accurate maintainer info
           nix-build trusted/ci -A eval.compare \
-            --arg beforeDir "$(realpath combinedTarget)" \
-            --arg afterDir "$(realpath combinedMerged)" \
+            --arg combinedDir "$(realpath ./combined)" \
             --arg touchedFilesJson ./touched-files.json \
             --argstr githubAuthorId "$AUTHOR_ID" \
             --out-link comparison
diff --git a/ci/eval/compare/default.nix b/ci/eval/compare/default.nix
index 01c735a4c218..f6cf1ebe7856 100644
--- a/ci/eval/compare/default.nix
+++ b/ci/eval/compare/default.nix
@@ -7,8 +7,7 @@
   python3,
 }:
 {
-  beforeDir,
-  afterDir,
+  combinedDir,
   touchedFilesJson,
   githubAuthorId,
   byName ? false,
@@ -66,7 +65,6 @@ let
       Example: { name = "python312Packages.numpy"; platform = "x86_64-linux"; }
   */
   inherit (import ./utils.nix { inherit lib; })
-    diff
     groupByKernel
     convertToPackagePlatformAttrs
     groupByPlatform
@@ -74,22 +72,10 @@ let
     getLabels
     ;
 
-  getAttrs =
-    dir:
-    let
-      raw = builtins.readFile "${dir}/outpaths.json";
-      # The file contains Nix paths; we need to ignore them for evaluation purposes,
-      # else there will be a "is not allowed to refer to a store path" error.
-      data = builtins.unsafeDiscardStringContext raw;
-    in
-    builtins.fromJSON data;
-  beforeAttrs = getAttrs beforeDir;
-  afterAttrs = getAttrs afterDir;
-
   # Attrs
   # - keys: "added", "changed" and "removed"
   # - values: lists of `packagePlatformPath`s
-  diffAttrs = diff beforeAttrs afterAttrs;
+  diffAttrs = builtins.fromJSON (builtins.readFile "${combinedDir}/combined-diff.json");
 
   rebuilds = diffAttrs.added ++ diffAttrs.changed;
   rebuildsPackagePlatformAttrs = convertToPackagePlatformAttrs rebuilds;
@@ -149,8 +135,8 @@ runCommand "compare"
     maintainers = builtins.toJSON maintainers;
     passAsFile = [ "maintainers" ];
     env = {
-      BEFORE_DIR = "${beforeDir}";
-      AFTER_DIR = "${afterDir}";
+      BEFORE_DIR = "${combinedDir}/before";
+      AFTER_DIR = "${combinedDir}/after";
     };
   }
   ''
diff --git a/ci/eval/compare/utils.nix b/ci/eval/compare/utils.nix
index 6e75b2a62790..064d2cf57ea1 100644
--- a/ci/eval/compare/utils.nix
+++ b/ci/eval/compare/utils.nix
@@ -93,32 +93,6 @@ rec {
     in
     uniqueStrings (builtins.map (p: p.name) packagePlatformAttrs);
 
-  /*
-    Computes the key difference between two attrs
-
-    {
-      added: [ <keys only in the second object> ],
-      removed: [ <keys only in the first object> ],
-      changed: [ <keys with different values between the two objects> ],
-    }
-  */
-  diff =
-    let
-      filterKeys = cond: attrs: lib.attrNames (lib.filterAttrs cond attrs);
-    in
-    old: new: {
-      added = filterKeys (n: _: !(old ? ${n})) new;
-      removed = filterKeys (n: _: !(new ? ${n})) old;
-      changed = filterKeys (
-        n: v:
-        # Filter out attributes that don't exist anymore
-        (new ? ${n})
-
-        # Filter out attributes that are the same as the new value
-        && (v != (new.${n}))
-      ) old;
-    };
-
   /*
     Group a list of `packagePlatformAttr`s by platforms
 
diff --git a/ci/eval/default.nix b/ci/eval/default.nix
index f60dd46efd3e..82f69e1c9a44 100644
--- a/ci/eval/default.nix
+++ b/ci/eval/default.nix
@@ -191,9 +191,11 @@ let
         cat "$chunkOutputDir"/result/* | jq -s 'add | map_values(.outputs)' > $out/${evalSystem}/paths.json
       '';
 
+  diff = callPackage ./diff.nix { };
+
   combine =
     {
-      evalDir,
+      diffDir,
     }:
     runCommand "combined-eval"
       {
@@ -205,12 +207,22 @@ let
         mkdir -p $out
 
         # Combine output paths from all systems
-        cat ${evalDir}/*/paths.json | jq -s add > $out/outpaths.json
+        cat ${diffDir}/*/diff.json | jq -s '
+          reduce .[] as $item ({}; {
+            added: (.added + $item.added),
+            changed: (.changed + $item.changed),
+            removed: (.removed + $item.removed)
+          })
+        ' > $out/combined-diff.json
 
-        mkdir -p $out/stats
+        mkdir -p $out/before/stats
+        for d in ${diffDir}/before/*; do
+          cp -r "$d"/stats-by-chunk $out/before/stats/$(basename "$d")
+        done
 
-        for d in ${evalDir}/*; do
-          cp -r "$d"/stats-by-chunk $out/stats/$(basename "$d")
+        mkdir -p $out/after/stats
+        for d in ${diffDir}/after/*; do
+          cp -r "$d"/stats-by-chunk $out/after/stats/$(basename "$d")
         done
       '';
 
@@ -225,18 +237,26 @@ let
       quickTest ? false,
     }:
     let
-      evals = symlinkJoin {
-        name = "evals";
+      diffs = symlinkJoin {
+        name = "diffs";
         paths = map (
           evalSystem:
-          singleSystem {
-            inherit quickTest evalSystem chunkSize;
+          let
+            eval = singleSystem {
+              inherit quickTest evalSystem chunkSize;
+            };
+          in
+          diff {
+            inherit evalSystem;
+            # Local "full" evaluation doesn't do a real diff.
+            beforeDir = eval;
+            afterDir = eval;
           }
         ) evalSystems;
       };
     in
     combine {
-      evalDir = evals;
+      diffDir = diffs;
     };
 
 in
@@ -244,6 +264,7 @@ in
   inherit
     attrpathsSuperset
     singleSystem
+    diff
     combine
     compare
     # The above three are used by separate VMs in a GitHub workflow,
diff --git a/ci/eval/diff.nix b/ci/eval/diff.nix
new file mode 100644
index 000000000000..629b4f8d3a6a
--- /dev/null
+++ b/ci/eval/diff.nix
@@ -0,0 +1,61 @@
+{
+  lib,
+  runCommand,
+  writeText,
+}:
+
+{
+  beforeDir,
+  afterDir,
+  evalSystem,
+}:
+
+let
+  /*
+    Computes the key difference between two attrs
+
+    {
+      added: [ <keys only in the second object> ],
+      removed: [ <keys only in the first object> ],
+      changed: [ <keys with different values between the two objects> ],
+    }
+  */
+  diff =
+    let
+      filterKeys = cond: attrs: lib.attrNames (lib.filterAttrs cond attrs);
+    in
+    old: new: {
+      added = filterKeys (n: _: !(old ? ${n})) new;
+      removed = filterKeys (n: _: !(new ? ${n})) old;
+      changed = filterKeys (
+        n: v:
+        # Filter out attributes that don't exist anymore
+        (new ? ${n})
+
+        # Filter out attributes that are the same as the new value
+        && (v != (new.${n}))
+      ) old;
+    };
+
+  getAttrs =
+    dir:
+    let
+      raw = builtins.readFile "${dir}/${evalSystem}/paths.json";
+      # The file contains Nix paths; we need to ignore them for evaluation purposes,
+      # else there will be a "is not allowed to refer to a store path" error.
+      data = builtins.unsafeDiscardStringContext raw;
+    in
+    builtins.fromJSON data;
+
+  beforeAttrs = getAttrs beforeDir;
+  afterAttrs = getAttrs afterDir;
+  diffAttrs = diff beforeAttrs afterAttrs;
+  diffJson = writeText "diff.json" (builtins.toJSON diffAttrs);
+in
+runCommand "diff" { } ''
+  mkdir -p $out/${evalSystem}
+
+  cp -r ${beforeDir} $out/before
+  cp -r ${afterDir} $out/after
+  cp ${diffJson} $out/${evalSystem}/diff.json
+''