diff --git a/apply.c b/apply.c
index 249248d4f205ca..4ce4160b48caf8 100644
--- a/apply.c
+++ b/apply.c
@@ -3893,7 +3893,7 @@ static int check_preimage(struct apply_state *state,
 		if (*ce && !(*ce)->ce_mode)
 			BUG("ce_mode == 0 for path '%s'", old_name);
 
-		if (trust_executable_bit || !S_ISREG(st->st_mode))
+		if (repo_trust_executable_bit(state->repo) || !S_ISREG(st->st_mode))
 			st_mode = ce_mode_from_stat(*ce, st->st_mode);
 		else if (*ce)
 			st_mode = (*ce)->ce_mode;
@@ -4511,7 +4511,7 @@ static int try_create_file(struct apply_state *state, const char *path,
 		return !!mkdir(path, 0777);
 	}
 
-	if (has_symlinks && S_ISLNK(mode))
+	if (repo_has_symlinks(state->repo) && S_ISLNK(mode))
 		/* Although buf:size is counted string, it also is NUL
 		 * terminated.
 		 */
diff --git a/combine-diff.c b/combine-diff.c
index b7998620687ed7..80e5c46e9b26ff 100644
--- a/combine-diff.c
+++ b/combine-diff.c
@@ -1078,7 +1078,7 @@ static void show_patch_diff(struct combine_diff_path *elem, int num_parent,
 			/* if symlinks don't work, assume symlink if all parents
 			 * are symlinks
 			 */
-			is_file = has_symlinks;
+			is_file = repo_has_symlinks(rev->repo);
 			for (i = 0; !is_file && i < num_parent; i++)
 				is_file = !S_ISLNK(elem->parent[i].mode);
 			if (!is_file)
diff --git a/compat/mingw.c b/compat/mingw.c
index aa7525f419cb64..47819119292d8e 100644
--- a/compat/mingw.c
+++ b/compat/mingw.c
@@ -7,6 +7,7 @@
 #include "config.h"
 #include "dir.h"
 #include "environment.h"
+#include "repository.h"
 #include "gettext.h"
 #include "run-command.h"
 #include "strbuf.h"
@@ -1043,7 +1044,7 @@ int mingw_chdir(const char *dirname)
 	if (xutftowcs_path(wdirname, dirname) < 0)
 		return -1;
 
-	if (has_symlinks) {
+	if (repo_has_symlinks(the_repository)) {
 		HANDLE hnd = CreateFileW(wdirname, 0,
 				FILE_SHARE_READ | FILE_SHARE_WRITE | FILE_SHARE_DELETE, NULL,
 				OPEN_EXISTING, FILE_FLAG_BACKUP_SEMANTICS, NULL);
@@ -2903,7 +2904,7 @@ int symlink(const char *target, const char *link)
 	int len;
 
 	/* fail if symlinks are disabled or API is not supported (WinXP) */
-	if (!has_symlinks) {
+	if (!repo_has_symlinks(the_repository)) {
 		errno = ENOSYS;
 		return -1;
 	}
@@ -3173,15 +3174,23 @@ static void setup_windows_environment(void)
 		if (!tmp && (tmp = getenv("USERPROFILE")))
 			setenv("HOME", tmp, 1);
 	}
+}
 
+int mingw_platform_has_symlinks(void)
+{
+	static int has_symlinks = -1;
 	/*
 	 * Change 'core.symlinks' default to false, unless native symlinks are
 	 * enabled in MSys2 (via 'MSYS=winsymlinks:nativestrict'). Thus we can
 	 * run the test suite (which doesn't obey config files) with or without
 	 * symlink support.
 	 */
-	if (!(tmp = getenv("MSYS")) || !strstr(tmp, "winsymlinks:nativestrict"))
-		has_symlinks = 0;
+	if (has_symlinks < 0) {
+		const char *tmp = getenv("MSYS");
+		has_symlinks = (tmp && strstr(tmp, "winsymlinks:nativestrict")) ? 1 : 0;
+	}
+
+	return has_symlinks;
 }
 
 static void get_current_user_sid(PSID *sid, HANDLE *linked_token)
diff --git a/compat/mingw.h b/compat/mingw.h
index 444daedfa52469..df02aeb632d8c3 100644
--- a/compat/mingw.h
+++ b/compat/mingw.h
@@ -208,6 +208,9 @@ void open_in_gdb(void);
  */
 int err_win_to_posix(DWORD winerr);
 
+int mingw_platform_has_symlinks(void);
+#define platform_has_symlinks() mingw_platform_has_symlinks()
+
 #ifndef NO_UNIX_SOCKETS
 int mingw_have_unix_sockets(void);
 #undef have_unix_sockets
diff --git a/entry.c b/entry.c
index 7817aee362ed9e..f2854b4cd8f122 100644
--- a/entry.c
+++ b/entry.c
@@ -321,7 +321,7 @@ static int write_entry(struct cache_entry *ce, char *path, struct conv_attrs *ca
 		 * We can't make a real symlink; write out a regular file entry
 		 * with the symlink destination as its contents.
 		 */
-		if (!has_symlinks || to_tempfile)
+		if (!repo_has_symlinks(state->istate ? state->istate->repo : NULL) || to_tempfile)
 			goto write_file_entry;
 
 		ret = symlink(new_blob, path);
diff --git a/environment.c b/environment.c
index fc3ed8bb1c7a66..760689d6e749de 100644
--- a/environment.c
+++ b/environment.c
@@ -41,10 +41,8 @@
 static int pack_compression_seen;
 static int zlib_compression_seen;
 
-int trust_executable_bit = 1;
 int trust_ctime = 1;
 int check_stat = 1;
-int has_symlinks = 1;
 int minimum_abbrev = 4, default_abbrev = -1;
 int ignore_case;
 int assume_unchanged;
@@ -142,6 +140,24 @@ int is_bare_repository(void)
 	return is_bare_repository_cfg && !repo_get_work_tree(the_repository);
 }
 
+int repo_trust_executable_bit(struct repository *repo)
+{
+	return repo->gitdir?
+		repo_config_values(repo)->trust_executable_bit :
+		1;
+}
+
+int repo_has_symlinks(struct repository *repo)
+{
+	if (!repo)
+		repo = the_repository;
+
+	if (!repo->gitdir)
+		return platform_has_symlinks();
+
+	return repo_config_values(repo)->has_symlinks;
+}
+
 int have_git_dir(void)
 {
 	return startup_info->have_repository
@@ -305,7 +321,7 @@ int git_default_core_config(const char *var, const char *value,
 
 	/* This needs a better name */
 	if (!strcmp(var, "core.filemode")) {
-		trust_executable_bit = git_config_bool(var, value);
+		cfg->trust_executable_bit = git_config_bool(var, value);
 		return 0;
 	}
 	if (!strcmp(var, "core.trustctime")) {
@@ -330,7 +346,8 @@ int git_default_core_config(const char *var, const char *value,
 	}
 
 	if (!strcmp(var, "core.symlinks")) {
-		has_symlinks = git_config_bool(var, value);
+		struct repo_config_values *cfg = repo_config_values(the_repository);
+		cfg->has_symlinks = git_config_bool(var, value);
 		return 0;
 	}
 
@@ -720,5 +737,7 @@ void repo_config_values_init(struct repo_config_values *cfg)
 {
 	cfg->attributes_file = NULL;
 	cfg->apply_sparse_checkout = 0;
+	cfg->trust_executable_bit = 1;
+	cfg->has_symlinks = platform_has_symlinks();
 	cfg->branch_track = BRANCH_TRACK_REMOTE;
 }
diff --git a/environment.h b/environment.h
index 123a71cdc8d14e..ef64a783b0f0fa 100644
--- a/environment.h
+++ b/environment.h
@@ -91,6 +91,8 @@ struct repo_config_values {
 	/* section "core" config values */
 	char *attributes_file;
 	int apply_sparse_checkout;
+	int trust_executable_bit;
+	int has_symlinks;
 
 	/* section "branch" config values */
 	enum branch_track branch_track;
@@ -123,6 +125,10 @@ int git_default_config(const char *, const char *,
 int git_default_core_config(const char *var, const char *value,
 			    const struct config_context *ctx, void *cb);
 
+int repo_trust_executable_bit(struct repository *repo);
+
+int repo_has_symlinks(struct repository *repo);
+
 void repo_config_values_init(struct repo_config_values *cfg);
 
 /*
@@ -160,10 +166,8 @@ int is_bare_repository(void);
 extern char *git_work_tree_cfg;
 
 /* Environment bits from configuration mechanism */
-extern int trust_executable_bit;
 extern int trust_ctime;
 extern int check_stat;
-extern int has_symlinks;
 extern int minimum_abbrev, default_abbrev;
 extern int ignore_case;
 extern int assume_unchanged;
diff --git a/git-compat-util.h b/git-compat-util.h
index 5024814bd48799..333a5acf33e6d1 100644
--- a/git-compat-util.h
+++ b/git-compat-util.h
@@ -245,6 +245,10 @@ static inline int git_is_dir_sep(int c)
 #define is_dir_sep git_is_dir_sep
 #endif
 
+#ifndef platform_has_symlinks
+#define platform_has_symlinks() 1
+#endif
+
 #ifndef offset_1st_component
 static inline int git_offset_1st_component(const char *path)
 {
diff --git a/read-cache.c b/read-cache.c
index 38a04b8de3d7fb..5a40ffa0611c06 100644
--- a/read-cache.c
+++ b/read-cache.c
@@ -202,15 +202,33 @@ void fill_stat_cache_info(struct index_state *istate, struct cache_entry *ce, st
 	}
 }
 
-static unsigned int st_mode_from_ce(const struct cache_entry *ce)
+/*
+ * Determine the appropriate index mode for a file based on its stat()
+ * information and the existing cache entry (if any).
+ *
+ * This function handles degradation for filesystems that lack
+ * symlink support or reliable executable bits.
+ */
+unsigned int ce_mode_from_stat(const struct cache_entry *ce, unsigned int mode)
 {
-	extern int trust_executable_bit, has_symlinks;
+	if (!repo_has_symlinks(the_repository) && S_ISREG(mode) &&
+	    ce && S_ISLNK(ce->ce_mode))
+		return ce->ce_mode;
+	if (!repo_trust_executable_bit(the_repository) && S_ISREG(mode)) {
+		if (ce && S_ISREG(ce->ce_mode))
+			return ce->ce_mode;
+		return create_ce_mode(0666);
+	}
+	return create_ce_mode(mode);
+}
 
+static unsigned int st_mode_from_ce(const struct cache_entry *ce)
+{
 	switch (ce->ce_mode & S_IFMT) {
 	case S_IFLNK:
-		return has_symlinks ? S_IFLNK : (S_IFREG | 0644);
+		return repo_has_symlinks(the_repository) ? S_IFLNK : (S_IFREG | 0644);
 	case S_IFREG:
-		return (ce->ce_mode & (trust_executable_bit ? 0755 : 0644)) | S_IFREG;
+		return (ce->ce_mode & (repo_trust_executable_bit(the_repository) ? 0755 : 0644)) | S_IFREG;
 	case S_IFGITLINK:
 		return S_IFDIR | 0755;
 	case S_IFDIR:
@@ -320,13 +338,13 @@ static int ce_match_stat_basic(const struct cache_entry *ce, struct stat *st)
 		/* We consider only the owner x bit to be relevant for
 		 * "mode changes"
 		 */
-		if (trust_executable_bit &&
+		if (repo_trust_executable_bit(the_repository) &&
 		    (0100 & (ce->ce_mode ^ st->st_mode)))
 			changed |= MODE_CHANGED;
 		break;
 	case S_IFLNK:
 		if (!S_ISLNK(st->st_mode) &&
-		    (has_symlinks || !S_ISREG(st->st_mode)))
+		    (repo_has_symlinks(the_repository) || !S_ISREG(st->st_mode)))
 			changed |= TYPE_CHANGED;
 		break;
 	case S_IFGITLINK:
@@ -741,7 +759,8 @@ int add_to_index(struct index_state *istate, const char *path, struct stat *st,
 		ce->ce_flags |= CE_INTENT_TO_ADD;
 
 
-	if (trust_executable_bit && has_symlinks) {
+	if (repo_trust_executable_bit(istate->repo) &&
+	    repo_has_symlinks(istate->repo)) {
 		ce->ce_mode = create_ce_mode(st_mode);
 	} else {
 		/* If there is an existing entry, pick the mode bits and type
diff --git a/read-cache.h b/read-cache.h
index 043da1f1aae706..3c4af2faeb5f78 100644
--- a/read-cache.h
+++ b/read-cache.h
@@ -5,20 +5,8 @@
 #include "object.h"
 #include "pathspec.h"
 
-static inline unsigned int ce_mode_from_stat(const struct cache_entry *ce,
-					     unsigned int mode)
-{
-	extern int trust_executable_bit, has_symlinks;
-	if (!has_symlinks && S_ISREG(mode) &&
-	    ce && S_ISLNK(ce->ce_mode))
-		return ce->ce_mode;
-	if (!trust_executable_bit && S_ISREG(mode)) {
-		if (ce && S_ISREG(ce->ce_mode))
-			return ce->ce_mode;
-		return create_ce_mode(0666);
-	}
-	return create_ce_mode(mode);
-}
+unsigned int ce_mode_from_stat(const struct cache_entry *ce,
+				unsigned int mode);
 
 static inline int ce_to_dtype(const struct cache_entry *ce)
 {