diff --git a/internal/pull/pull.go b/internal/pull/pull.go
index c45f79e..4ce5ee5 100644
--- a/internal/pull/pull.go
+++ b/internal/pull/pull.go
@@ -9,6 +9,7 @@ import (
 	"net/http"
 	"os"
 	"regexp"
+	"strings"
 
 	log "github.com/sirupsen/logrus"
 
@@ -90,6 +91,35 @@ func (pullService *pullService) pullGit(fresh bool) error {
 		}
 	}
 
+	remote, err := localRepository.Remote(git.DefaultRemoteName)
+	if err != nil {
+		return errors.Wrap(err, "Error getting remote.")
+	}
+	remoteReferences, err := remote.List(&git.ListOptions{Auth: credentials})
+	if err != nil {
+		return errors.Wrap(err, "Error listing remote references.")
+	}
+	localReferences, err := localRepository.References()
+	if err != nil {
+		return errors.Wrap(err, "Error listing local references.")
+	}
+	localReferences.ForEach(func(localReference *plumbing.Reference) error {
+		if !strings.HasPrefix(localReference.Name().String(), "refs/") {
+			return nil
+		}
+		for _, remoteReference := range remoteReferences {
+			remoteReferenceName := strings.TrimPrefix(remoteReference.Name().String(), "refs/")
+			if cachedirectory.CacheReferencePrefix+remoteReferenceName == localReference.Name().String() {
+				return nil
+			}
+		}
+		err := localRepository.Storer.RemoveReference(localReference.Name())
+		if err != nil {
+			return errors.Wrap(err, "Error pruning reference.")
+		}
+		return nil
+	})
+
 	err = localRepository.FetchContext(pullService.ctx, &git.FetchOptions{
 		RemoteName: git.DefaultRemoteName,
 		RefSpecs: []config.RefSpec{
diff --git a/internal/pull/pull_test.go b/internal/pull/pull_test.go
index af4572e..215411a 100644
--- a/internal/pull/pull_test.go
+++ b/internal/pull/pull_test.go
@@ -94,6 +94,7 @@ func TestPullGitFresh(t *testing.T) {
 		// It is expected that we still pull these even though they don't match the expected pattern. We just ignore them later on.
 		"bd82b85707bc13904e3526517677039d4da4a9bb refs/remotes/origin/heads/very-ignored-branch",
 		"bd82b85707bc13904e3526517677039d4da4a9bb refs/remotes/origin/tags/an-ignored-tag-too",
+		"26936381e619a01122ea33993e3cebc474496805 refs/remotes/origin/heads/a-ref-that-will-need-pruning",
 	})
 }
 
@@ -125,11 +126,9 @@ func TestPullGitNotFreshWithChanges(t *testing.T) {
 		"b9f01aa2c50f49898d4c7845a66be8824499fe9d refs/remotes/origin/heads/main",
 		"26936381e619a01122ea33993e3cebc474496805 refs/remotes/origin/heads/v1",
 		"33d42021633d74bcd0bf9c95e3d3159131a5faa7 refs/remotes/origin/heads/v3", // v3 was force-pushed, and should have been force-pulled too.
-		"26936381e619a01122ea33993e3cebc474496805 refs/remotes/origin/tags/v2",
 		"42d077b4730d1ba413f7bb7e0fa7c98653fb0c78 refs/remotes/origin/heads/v4", // v4 is a new branch.
-		// We deleted these, but we don't currently do any pruning.
-		"bd82b85707bc13904e3526517677039d4da4a9bb refs/remotes/origin/heads/very-ignored-branch",
 		"bd82b85707bc13904e3526517677039d4da4a9bb refs/remotes/origin/tags/an-ignored-tag-too",
+		"26936381e619a01122ea33993e3cebc474496805 refs/remotes/origin/heads/a-ref-that-will-need-pruning/because-it-now-has-this-extra-bit",
 	})
 }
 
diff --git a/internal/pull/pull_test/codeql-action-initial.git/packed-refs b/internal/pull/pull_test/codeql-action-initial.git/packed-refs
index 3cbd2b2..35fceb0 100644
--- a/internal/pull/pull_test/codeql-action-initial.git/packed-refs
+++ b/internal/pull/pull_test/codeql-action-initial.git/packed-refs
@@ -1,4 +1,5 @@
 # pack-refs with: peeled fully-peeled sorted 
+26936381e619a01122ea33993e3cebc474496805 refs/heads/a-ref-that-will-need-pruning
 b9f01aa2c50f49898d4c7845a66be8824499fe9d refs/heads/main
 26936381e619a01122ea33993e3cebc474496805 refs/heads/v1
 e529a54fad10a936308b2220e05f7f00757f8e7c refs/heads/v3
diff --git a/internal/pull/pull_test/codeql-action-modified.git/packed-refs b/internal/pull/pull_test/codeql-action-modified.git/packed-refs
index 16ae202..059f1b6 100644
--- a/internal/pull/pull_test/codeql-action-modified.git/packed-refs
+++ b/internal/pull/pull_test/codeql-action-modified.git/packed-refs
@@ -1,6 +1,7 @@
 # pack-refs with: peeled fully-peeled sorted 
+26936381e619a01122ea33993e3cebc474496805 refs/heads/a-ref-that-will-need-pruning/because-it-now-has-this-extra-bit
 b9f01aa2c50f49898d4c7845a66be8824499fe9d refs/heads/main
 26936381e619a01122ea33993e3cebc474496805 refs/heads/v1
 33d42021633d74bcd0bf9c95e3d3159131a5faa7 refs/heads/v3
 42d077b4730d1ba413f7bb7e0fa7c98653fb0c78 refs/heads/v4
-26936381e619a01122ea33993e3cebc474496805 refs/tags/v2
+bd82b85707bc13904e3526517677039d4da4a9bb refs/tags/an-ignored-tag-too