diff --git a/branches.go b/branches.go
index 6a0c8af..0fe4435 100644
--- a/branches.go
+++ b/branches.go
@@ -4,6 +4,7 @@ import (
 	"fmt"
 	"os"
 	"path/filepath"
+	"strings"
 
 	"github.com/ghodss/yaml"
 	"github.com/pkg/errors"
@@ -145,7 +146,10 @@ func switchToCommitBranch(rc requestContext) (string, error) {
 	}
 
 	// Clean the branch so we can replace its contents wholesale
-	if err := cleanCommitBranch(rc.repo.WorkingDir()); err != nil {
+	if err := cleanCommitBranch(
+		rc.repo.WorkingDir(),
+		rc.target.branchConfig.PreservedPaths,
+	); err != nil {
 		return "", errors.Wrap(err, "error cleaning commit branch")
 	}
 	logger.Debug("cleaned commit branch")
@@ -154,19 +158,77 @@ func switchToCommitBranch(rc requestContext) (string, error) {
 }
 
 // cleanCommitBranch deletes the entire contents of the specified directory
-// EXCEPT for the .git and .kargo-render subdirectories.
-func cleanCommitBranch(dir string) error {
-	dirEntries, err := os.ReadDir(dir)
+// EXCEPT for the paths specified by preservedPaths.
+func cleanCommitBranch(dir string, preservedPaths []string) error {
+	_, err := cleanDir(
+		dir,
+		normalizePreservedPaths(
+			dir,
+			append(preservedPaths, ".git", ".kargo-render"),
+		),
+	)
+	return err
+}
+
+// normalizePreservedPaths converts the relative paths in the preservedPaths
+// argument to absolute paths relative to the workingDir argument. It also
+// removes any trailing path separators from the paths.
+func normalizePreservedPaths(
+	workingDir string,
+	preservedPaths []string,
+) []string {
+	normalizedPreservedPaths := make([]string, len(preservedPaths))
+	for i, preservedPath := range preservedPaths {
+		if strings.HasSuffix(preservedPath, string(os.PathSeparator)) {
+			preservedPath = preservedPath[:len(preservedPath)-1]
+		}
+		normalizedPreservedPaths[i] = filepath.Join(workingDir, preservedPath)
+	}
+	return normalizedPreservedPaths
+}
+
+// cleanDir recursively deletes the entire contents of the directory specified
+// by the absolute path dir EXCEPT for any paths specified by the preservedPaths
+// argument. The function returns true if dir is left empty afterwards and false
+// otherwise.
+func cleanDir(dir string, preservedPaths []string) (bool, error) {
+	items, err := os.ReadDir(dir)
 	if err != nil {
-		return err
+		return false, err
 	}
-	for _, dirEntry := range dirEntries {
-		if dirEntry.Name() == ".git" || dirEntry.Name() == ".kargo-render" {
+	for _, item := range items {
+		path := filepath.Join(dir, item.Name())
+		if isPathPreserved(path, preservedPaths) {
 			continue
 		}
-		if err = os.RemoveAll(filepath.Join(dir, dirEntry.Name())); err != nil {
-			return err
+		if item.IsDir() {
+			var isEmpty bool
+			if isEmpty, err = cleanDir(path, preservedPaths); err != nil {
+				return false, err
+			}
+			if isEmpty {
+				if err = os.Remove(path); err != nil {
+					return false, err
+				}
+			}
+		} else if err = os.Remove(path); err != nil {
+			return false, err
 		}
 	}
-	return nil
+	if items, err = os.ReadDir(dir); err != nil {
+		return false, err
+	}
+	return len(items) == 0, nil
+}
+
+// isPathPreserved returns true if the specified path is among those specified
+// by the preservedPaths argument. Both path and preservedPaths MUST be absolute
+// paths. Paths to directories MUST NOT end with a trailing path separator.
+func isPathPreserved(path string, preservedPaths []string) bool {
+	for _, preservedPath := range preservedPaths {
+		if path == preservedPath {
+			return true
+		}
+	}
+	return false
 }
diff --git a/branches_test.go b/branches_test.go
index f38c47b..9750eae 100644
--- a/branches_test.go
+++ b/branches_test.go
@@ -107,7 +107,7 @@ func TestCleanCommitBranch(t *testing.T) {
 	require.NoError(t, err)
 	require.Len(t, dirEntries, subdirCount+fileCount+2)
 	// Delete
-	err = cleanCommitBranch(dir)
+	err = cleanCommitBranch(dir, []string{})
 	require.NoError(t, err)
 	// .git should not have been deleted
 	_, err = os.Stat(filepath.Join(dir, ".git"))
@@ -121,6 +121,107 @@ func TestCleanCommitBranch(t *testing.T) {
 	require.Len(t, dirEntries, 2)
 }
 
+func TestNormalizePreservedPaths(t *testing.T) {
+	preservedPaths := []string{
+		"foo/bar",
+		"bat/baz/",
+	}
+	normalizedPreservedPaths :=
+		normalizePreservedPaths("fake-work-dir", preservedPaths)
+	require.Equal(
+		t,
+		[]string{
+			filepath.Join("fake-work-dir", "foo", "bar"),
+			filepath.Join("fake-work-dir", "bat", "baz"),
+		},
+		normalizedPreservedPaths,
+	)
+}
+
+func TestCleanDir(t *testing.T) {
+	dir, err := os.MkdirTemp("", "")
+	defer os.RemoveAll(dir)
+	require.NoError(t, err)
+
+	// This is what the test directory structure will look like:
+	// .
+	// ├── foo            preserved directly
+	// │   └── foo.txt    preserved because foo is
+	// ├── bar            preserved because bar/bar.txt is
+	// │   └── bar.txt    preserved directly
+	// ├── baz            deleted because empty
+	// │   └── baz.txt    deleted
+	// └── keep.txt       preserved directly
+
+	// Create the test directory structure
+	fooDir := filepath.Join(dir, "foo")
+	err = os.Mkdir(fooDir, 0755)
+	require.NoError(t, err)
+	fooFile := filepath.Join(fooDir, "foo.txt")
+	err = os.WriteFile(fooFile, []byte("foo"), 0600)
+	require.NoError(t, err)
+
+	barDir := filepath.Join(dir, "bar")
+	err = os.Mkdir(barDir, 0755)
+	require.NoError(t, err)
+	barFile := filepath.Join(barDir, "bar.txt")
+	err = os.WriteFile(barFile, []byte("bar"), 0600)
+	require.NoError(t, err)
+
+	bazDir := filepath.Join(dir, "baz")
+	err = os.Mkdir(bazDir, 0755)
+	require.NoError(t, err)
+	bazFile := filepath.Join(bazDir, "baz.txt")
+	err = os.WriteFile(bazFile, []byte("baz"), 0600)
+	require.NoError(t, err)
+
+	keepFile := filepath.Join(dir, "keep.txt")
+	err = os.WriteFile(keepFile, []byte("keep"), 0600)
+	require.NoError(t, err)
+
+	preservedPaths := []string{
+		fooDir,
+		barFile,
+		keepFile,
+	}
+
+	isEmpty, err := cleanDir(dir, preservedPaths)
+	require.NoError(t, err)
+	require.False(t, isEmpty)
+
+	// Validate what was deleted and what wasn't
+
+	// All of foo/ remains
+	_, err = os.Stat(fooDir)
+	require.NoError(t, err)
+	_, err = os.Stat(fooFile)
+	require.NoError(t, err)
+
+	// All of bar/ remains
+	_, err = os.Stat(barDir)
+	require.NoError(t, err)
+	_, err = os.Stat(barFile)
+	require.NoError(t, err)
+
+	// All of baz/ is gone
+	_, err = os.Stat(bazDir)
+	require.True(t, os.IsNotExist(err))
+
+	// keep.txt remains
+	_, err = os.Stat(keepFile)
+	require.NoError(t, err)
+}
+
+func TestIsPathPreserved(t *testing.T) {
+	preservedPaths := []string{
+		"/foo/bar",
+		"/foo/bat",
+	}
+	require.True(t, isPathPreserved("/foo/bar", preservedPaths))
+	require.True(t, isPathPreserved("/foo/bat", preservedPaths))
+	require.False(t, isPathPreserved("/foo/baz", preservedPaths))
+}
+
 func createDummyCommitBranchDir(dirCount, fileCount int) (string, error) {
 	// Create a directory
 	dir, err := os.MkdirTemp("", "")
diff --git a/config.go b/config.go
index c521a79..cffa6de 100644
--- a/config.go
+++ b/config.go
@@ -69,6 +69,15 @@ type branchConfig struct {
 	// PRs encapsulates details about how to manage any pull requests associated
 	// with this branch.
 	PRs pullRequestConfig `json:"prs,omitempty"`
+	// PreservedPaths specifies paths relative to the root of the repository that
+	// should be exempted from pre-render cleaning (deletion) of
+	// environment-specific branch contents. This is useful for preserving any
+	// environment-specific files that are manually maintained. Typically there
+	// are very few such files, if any at all, with an environment-specific
+	// CODEOWNERS file at the root of the repository being the most emblematic
+	// exception. Paths may be to files or directories. Any path to a directory
+	// will cause that directory's entire contents to be preserved.
+	PreservedPaths []string `json:"preservedPaths,omitempty"`
 }
 
 func (b branchConfig) expand(values []string) branchConfig {
@@ -77,6 +86,9 @@ func (b branchConfig) expand(values []string) branchConfig {
 	for appName, appConfig := range b.AppConfigs {
 		cfg.AppConfigs[appName] = appConfig.expand(values)
 	}
+	for i, path := range b.PreservedPaths {
+		b.PreservedPaths[i] = file.ExpandPath(path, values)
+	}
 	return cfg
 }
 
diff --git a/schema.json b/schema.json
index 6db64b9..2c1a858 100644
--- a/schema.json
+++ b/schema.json
@@ -40,6 +40,12 @@
 				},
 				"prs": {
 					"$ref": "#/definitions/pullRequestConfig"
+				},
+				"preservedPaths": {
+					"type": "array",
+					"items": {
+						"$ref": "#/definitions/relativePath"
+					}
 				}
 			}
 		},