diff --git a/config/internal.go b/config/internal.go
index 267bb250f..8341a9149 100644
--- a/config/internal.go
+++ b/config/internal.go
@@ -6,6 +6,14 @@ type Internal struct {
 	UnixFSShardingSizeThreshold *OptionalString   `json:",omitempty"` // moved to Import.UnixFSHAMTDirectorySizeThreshold
 	Libp2pForceReachability     *OptionalString   `json:",omitempty"`
 	BackupBootstrapInterval     *OptionalDuration `json:",omitempty"`
+	// MFSAutoflushThreshold controls the number of entries cached in memory
+	// for each MFS directory before auto-flush is triggered to prevent
+	// unbounded memory growth when using --flush=false.
+	// Default: 256 (matches HAMT shard size)
+	// Set to 0 to disable cache limiting (old behavior, may cause high memory usage)
+	// This is an EXPERIMENTAL feature and may change or be removed in future releases.
+	// See https://github.com/ipfs/kubo/issues/10842
+	MFSAutoflushThreshold OptionalInteger `json:",omitempty"`
 }
 
 type InternalBitswap struct {
diff --git a/core/commands/files.go b/core/commands/files.go
index 12a96eba2..35cdff6ee 100644
--- a/core/commands/files.go
+++ b/core/commands/files.go
@@ -64,13 +64,16 @@ defaults to true and ensures two things: 1) that the changes are reflected in
 the full MFS structure (updated CIDs) 2) that the parent-folder's cache is
 cleared. Use caution when setting this flag to false. It will improve
 performance for large numbers of file operations, but it does so at the cost
-of consistency guarantees and unbound growth of the directories' in-memory
-caches.  If the daemon is unexpectedly killed before running 'ipfs files
-flush' on the files in question, then data may be lost. This also applies to
-run 'ipfs repo gc' concurrently with '--flush=false' operations. We recommend
-flushing paths regularly with 'ipfs files flush', specially the folders on
-which many write operations are happening, as a way to clear the directory
-cache, free memory and speed up read operations.`,
+of consistency guarantees. If the daemon is unexpectedly killed before running
+'ipfs files flush' on the files in question, then data may be lost. This also
+applies to run 'ipfs repo gc' concurrently with '--flush=false' operations.
+
+When using '--flush=false', directories will automatically flush when the
+number of cached entries exceeds the Internal.MFSAutoflushThreshold config.
+This prevents unbounded memory growth. We recommend flushing
+paths regularly with 'ipfs files flush', specially the folders on which many
+write operations are happening, as a way to clear the directory cache, free
+memory and speed up read operations.`,
 	},
 	Options: []cmds.Option{
 		cmds.BoolOption(filesFlushOptionName, "f", "Flush target and ancestors after write.").WithDefault(true),
@@ -1258,6 +1261,13 @@ Remove files or directories.
 		cmds.BoolOption(forceOptionName, "Forcibly remove target at path; implies -r for directories"),
 	},
 	Run: func(req *cmds.Request, res cmds.ResponseEmitter, env cmds.Environment) error {
+		// Check if user explicitly set --flush=false
+		if flushOpt, ok := req.Options[filesFlushOptionName]; ok {
+			if flush, ok := flushOpt.(bool); ok && !flush {
+				return fmt.Errorf("files rm always flushes for safety. The --flush flag cannot be set to false for this command")
+			}
+		}
+
 		nd, err := cmdenv.GetNode(env)
 		if err != nil {
 			return err
diff --git a/core/node/core.go b/core/node/core.go
index 5ad1e557b..7cafe302e 100644
--- a/core/node/core.go
+++ b/core/node/core.go
@@ -242,6 +242,16 @@ func Files(strategy string) func(mctx helpers.MetricsCtx, lc fx.Lifecycle, repo
 		}
 
 		root, err := mfs.NewRoot(ctx, dag, nd, pf, prov)
+		if err != nil {
+			return nil, err
+		}
+
+		// Configure MFS directory cache auto-flush threshold if specified (experimental)
+		cfg, err := repo.Config()
+		if err == nil && !cfg.Internal.MFSAutoflushThreshold.IsDefault() {
+			threshold := int(cfg.Internal.MFSAutoflushThreshold.WithDefault(int64(mfs.DefaultMaxCacheSize)))
+			root.SetMaxCacheSize(threshold)
+		}
 
 		lc.Append(fx.Hook{
 			OnStop: func(ctx context.Context) error {
diff --git a/docs/changelogs/v0.38.md b/docs/changelogs/v0.38.md
index 440ee0f9d..ccf60730d 100644
--- a/docs/changelogs/v0.38.md
+++ b/docs/changelogs/v0.38.md
@@ -81,6 +81,10 @@ Identity CIDs use [multihash `0x00`](https://github.com/multiformats/multicodec/
 
 This release resolves several long-standing MFS issues: raw nodes now preserve their codec instead of being forced to dag-pb, append operations on raw nodes work correctly by converting to UnixFS when needed, and identity CIDs properly inherit the full CID prefix from parent directories.
 
+#### MFS directory cache auto-flush
+
+The new [`Internal.MFSAutoflushThreshold`](https://github.com/ipfs/kubo/blob/master/docs/config.md#internalmfsautoflushthreshold) configuration option prevents unbounded memory growth when using `--flush=false` with `ipfs files` commands by automatically flushing directories when their cache exceeds the configured threshold (default: 256 entries).
+
 ### 📦️ Important dependency updates
 
 ### 📝 Changelog
diff --git a/docs/config.md b/docs/config.md
index ef3d8ad63..9ef96514d 100644
--- a/docs/config.md
+++ b/docs/config.md
@@ -1599,6 +1599,31 @@ Type: `flag`
 
 **MOVED:** see [`Import.UnixFSHAMTDirectorySizeThreshold`](#importunixfshamtdirectorysizethreshold)
 
+### `Internal.MFSAutoflushThreshold`
+
+Controls the number of entries cached in memory for each MFS directory before
+auto-flush is triggered to prevent unbounded memory growth when using `--flush=false`
+with `ipfs files` commands.
+
+When a directory's cache reaches this threshold, it will automatically flush to
+the blockstore even when `--flush=false` is specified. This prevents excessive
+memory usage while still allowing performance benefits of deferred flushing for
+smaller operations.
+
+**Examples:**
+* `256` - Default value. Provides a good balance between performance and memory usage.
+* `0` - Disables cache limiting (behavior before Kubo 0.38). May cause high memory
+  usage with `--flush=false` on large directories.
+* `1024` - Higher limit for systems with more available memory that need to perform
+  many operations before flushing.
+
+Default: `256`
+
+Type: `optionalInteger` (0 disables the limit, risky, may lead to errors)
+
+**Note:** This is an EXPERIMENTAL feature and may change or be removed in future releases.
+See [#10842](https://github.com/ipfs/kubo/issues/10842) for more information.
+
 ## `Ipns`
 
 ### `Ipns.RepublishPeriod`
diff --git a/test/cli/files_test.go b/test/cli/files_test.go
index 275261897..91589ea9c 100644
--- a/test/cli/files_test.go
+++ b/test/cli/files_test.go
@@ -118,3 +118,63 @@ func TestFilesCp(t *testing.T) {
 		assert.Equal(t, data, catRes.Stdout.Trimmed())
 	})
 }
+
+func TestFilesRm(t *testing.T) {
+	t.Parallel()
+
+	t.Run("files rm with --flush=false returns error", func(t *testing.T) {
+		// Test that files rm rejects --flush=false so user does not assume disabling flush works
+		// (rm ignored it before, better to explicitly error)
+		// See https://github.com/ipfs/kubo/issues/10842
+		t.Parallel()
+
+		node := harness.NewT(t).NewNode().Init().StartDaemon()
+
+		// Create a file to remove
+		node.IPFS("files", "mkdir", "/test-dir")
+
+		// Try to remove with --flush=false, should error
+		res := node.RunIPFS("files", "rm", "-r", "--flush=false", "/test-dir")
+		assert.NotEqual(t, 0, res.ExitErr.ExitCode())
+		assert.Contains(t, res.Stderr.String(), "files rm always flushes for safety")
+		assert.Contains(t, res.Stderr.String(), "cannot be set to false")
+
+		// Verify the directory still exists (wasn't removed due to error)
+		lsRes := node.IPFS("files", "ls", "/")
+		assert.Contains(t, lsRes.Stdout.String(), "test-dir")
+	})
+
+	t.Run("files rm with --flush=true works", func(t *testing.T) {
+		t.Parallel()
+
+		node := harness.NewT(t).NewNode().Init().StartDaemon()
+
+		// Create a file to remove
+		node.IPFS("files", "mkdir", "/test-dir")
+
+		// Remove with explicit --flush=true, should work
+		res := node.IPFS("files", "rm", "-r", "--flush=true", "/test-dir")
+		assert.NoError(t, res.Err)
+
+		// Verify the directory was removed
+		lsRes := node.IPFS("files", "ls", "/")
+		assert.NotContains(t, lsRes.Stdout.String(), "test-dir")
+	})
+
+	t.Run("files rm without flush flag works (default behavior)", func(t *testing.T) {
+		t.Parallel()
+
+		node := harness.NewT(t).NewNode().Init().StartDaemon()
+
+		// Create a file to remove
+		node.IPFS("files", "mkdir", "/test-dir")
+
+		// Remove without flush flag (should use default which is true)
+		res := node.IPFS("files", "rm", "-r", "/test-dir")
+		assert.NoError(t, res.Err)
+
+		// Verify the directory was removed
+		lsRes := node.IPFS("files", "ls", "/")
+		assert.NotContains(t, lsRes.Stdout.String(), "test-dir")
+	})
+}