diff --git a/internal/checker/checker.go b/internal/checker/checker.go
index d5e7fd1f8..031e13807 100644
--- a/internal/checker/checker.go
+++ b/internal/checker/checker.go
@@ -146,7 +146,11 @@ func (c *Checker) LoadIndex(ctx context.Context, p *progress.Counter) (hints []e
 		return hints, append(errs, err)
 	}
 
-	c.repo.SetIndex(c.masterIndex)
+	err = c.repo.SetIndex(c.masterIndex)
+	if err != nil {
+		debug.Log("SetIndex returned error: %v", err)
+		errs = append(errs, err)
+	}
 
 	// compute pack size using index entries
 	c.packs, err = pack.Size(ctx, c.repo, false)
diff --git a/internal/repository/repair_index.go b/internal/repository/repair_index.go
index c72dcfd00..770809254 100644
--- a/internal/repository/repair_index.go
+++ b/internal/repository/repair_index.go
@@ -52,8 +52,10 @@ func RepairIndex(ctx context.Context, repo *Repository, opts RepairIndexOptions,
 			return err
 		}
 
-		repo.SetIndex(mi)
-
+		err = repo.SetIndex(mi)
+		if err != nil {
+			return err
+		}
 		packSizeFromIndex, err = pack.Size(ctx, repo, false)
 		if err != nil {
 			return err
diff --git a/internal/repository/repository.go b/internal/repository/repository.go
index 3dc248c5e..f7fd65c71 100644
--- a/internal/repository/repository.go
+++ b/internal/repository/repository.go
@@ -6,6 +6,7 @@ import (
 	"fmt"
 	"io"
 	"math"
+	"os"
 	"runtime"
 	"sort"
 	"sync"
@@ -585,8 +586,9 @@ func (r *Repository) ListPacksFromIndex(ctx context.Context, packs restic.IDSet)
 }
 
 // SetIndex instructs the repository to use the given index.
-func (r *Repository) SetIndex(i restic.MasterIndex) {
+func (r *Repository) SetIndex(i restic.MasterIndex) error {
 	r.idx = i.(*index.MasterIndex)
+	return r.prepareCache()
 }
 
 func (r *Repository) clearIndex() {
@@ -626,8 +628,12 @@ func (r *Repository) LoadIndex(ctx context.Context, p *progress.Counter) error {
 			return errors.New("index uses feature not supported by repository version 1")
 		}
 	}
+	if ctx.Err() != nil {
+		return ctx.Err()
+	}
 
-	return ctx.Err()
+	// remove index files from the cache which have been removed in the repo
+	return r.prepareCache()
 }
 
 // createIndexFromPacks creates a new index by reading all given pack files (with sizes).
@@ -693,6 +699,33 @@ func (r *Repository) createIndexFromPacks(ctx context.Context, packsize map[rest
 	return invalid, nil
 }
 
+// prepareCache initializes the local cache. indexIDs is the list of IDs of
+// index files still present in the repo.
+func (r *Repository) prepareCache() error {
+	if r.Cache == nil {
+		return nil
+	}
+
+	indexIDs := r.idx.IDs()
+	debug.Log("prepare cache with %d index files", len(indexIDs))
+
+	// clear old index files
+	err := r.Cache.Clear(restic.IndexFile, indexIDs)
+	if err != nil {
+		fmt.Fprintf(os.Stderr, "error clearing index files in cache: %v\n", err)
+	}
+
+	packs := r.idx.Packs(restic.NewIDSet())
+
+	// clear old packs
+	err = r.Cache.Clear(restic.PackFile, packs)
+	if err != nil {
+		fmt.Fprintf(os.Stderr, "error clearing pack files in cache: %v\n", err)
+	}
+
+	return nil
+}
+
 // SearchKey finds a key with the supplied password, afterwards the config is
 // read and parsed. It tries at most maxKeys key files in the repo.
 func (r *Repository) SearchKey(ctx context.Context, password string, maxKeys int, keyHint string) error {
diff --git a/internal/restic/repository.go b/internal/restic/repository.go
index ce8401b37..b18b036a7 100644
--- a/internal/restic/repository.go
+++ b/internal/restic/repository.go
@@ -22,7 +22,7 @@ type Repository interface {
 	Key() *crypto.Key
 
 	LoadIndex(ctx context.Context, p *progress.Counter) error
-	SetIndex(mi MasterIndex)
+	SetIndex(mi MasterIndex) error
 
 	LookupBlob(t BlobType, id ID) []PackedBlob
 	LookupBlobSize(t BlobType, id ID) (size uint, exists bool)