diff --git a/doc/man1/notmuch-config.rst b/doc/man1/notmuch-config.rst
index bc597957..223d2de5 100644
--- a/doc/man1/notmuch-config.rst
+++ b/doc/man1/notmuch-config.rst
@@ -43,13 +43,22 @@ configuration file and corresponding database.
 The available configuration items are described below.
 
 **database.path**
-    The top-level directory where your mail currently exists and to
-    where mail will be delivered in the future. Files should be
-    individual email messages. Notmuch will store its database within
-    a sub-directory of the path configured here named ``.notmuch``.
+    Notmuch will store its database here, (in
+    sub-directory named ``.notmuch`` if **database.mail\_root**
+    is unset).
 
     Default: ``$MAILDIR`` variable if set, otherwise ``$HOME/mail``.
 
+**database.mail_root**
+    The top-level directory where your mail currently exists and to
+    where mail will be delivered in the future. Files should be
+    individual email messages.
+
+    History: this configuration value was introduced in notmuch 0.32.
+
+    Default: For compatibility with older configurations, the value of
+    database.path is used if **database.mail\_root** is unset.
+
 **database.hook_dir**
 
     Directory containing hooks run by notmuch commands. See
diff --git a/lib/config.cc b/lib/config.cc
index 483a02ef..f2060e28 100644
--- a/lib/config.cc
+++ b/lib/config.cc
@@ -406,6 +406,8 @@ _notmuch_config_key_to_string (notmuch_config_key_t key)
     switch (key) {
     case NOTMUCH_CONFIG_DATABASE_PATH:
 	return "database.path";
+    case NOTMUCH_CONFIG_MAIL_ROOT:
+	return "database.mail_root";
     case NOTMUCH_CONFIG_HOOK_DIR:
 	return "database.hook_dir";
     case NOTMUCH_CONFIG_EXCLUDE_TAGS:
@@ -428,7 +430,7 @@ _notmuch_config_key_to_string (notmuch_config_key_t key)
 }
 
 static const char *
-_notmuch_config_default (void *ctx, notmuch_config_key_t key)
+_notmuch_config_default (notmuch_database_t *notmuch, notmuch_config_key_t key)
 {
     char *path;
 
@@ -436,11 +438,14 @@ _notmuch_config_default (void *ctx, notmuch_config_key_t key)
     case NOTMUCH_CONFIG_DATABASE_PATH:
 	path = getenv ("MAILDIR");
 	if (path)
-	    path = talloc_strdup (ctx, path);
+	    path = talloc_strdup (notmuch, path);
 	else
-	    path = talloc_asprintf (ctx, "%s/mail",
+	    path = talloc_asprintf (notmuch, "%s/mail",
 				    getenv ("HOME"));
 	return path;
+    case NOTMUCH_CONFIG_MAIL_ROOT:
+	/* by default, mail root is the same as database path */
+	return notmuch_database_get_path (notmuch);
     case NOTMUCH_CONFIG_EXCLUDE_TAGS:
 	return "";
     case NOTMUCH_CONFIG_NEW_TAGS:
diff --git a/lib/database.cc b/lib/database.cc
index 580b2d58..248d1dc2 100644
--- a/lib/database.cc
+++ b/lib/database.cc
@@ -1350,7 +1350,7 @@ _notmuch_database_relative_path (notmuch_database_t *notmuch,
     const char *db_path, *relative;
     unsigned int db_path_len;
 
-    db_path = notmuch_database_get_path (notmuch);
+    db_path = notmuch_config_get (notmuch, NOTMUCH_CONFIG_MAIL_ROOT);
     db_path_len = strlen (db_path);
 
     relative = path;
diff --git a/lib/message-file.c b/lib/message-file.c
index 15b0bfad..9e9b387f 100644
--- a/lib/message-file.c
+++ b/lib/message-file.c
@@ -64,7 +64,7 @@ _notmuch_message_file_open_ctx (notmuch_database_t *notmuch,
     if (unlikely (message == NULL))
 	return NULL;
 
-    const char *prefix = notmuch_database_get_path (notmuch);
+    const char *prefix = notmuch_config_get (notmuch, NOTMUCH_CONFIG_MAIL_ROOT);
 
     if (prefix == NULL)
 	goto FAIL;
diff --git a/lib/message.cc b/lib/message.cc
index 73a7805f..0c2eeab5 100644
--- a/lib/message.cc
+++ b/lib/message.cc
@@ -1102,7 +1102,7 @@ _notmuch_message_ensure_filename_list (notmuch_message_t *message)
 
 	*colon = '\0';
 
-	db_path = notmuch_database_get_path (message->notmuch);
+	db_path = notmuch_config_get (message->notmuch, NOTMUCH_CONFIG_MAIL_ROOT);
 
 	directory = _notmuch_database_get_directory_path (local,
 							  message->notmuch,
diff --git a/lib/notmuch.h b/lib/notmuch.h
index b5688087..c9b01719 100644
--- a/lib/notmuch.h
+++ b/lib/notmuch.h
@@ -2474,6 +2474,7 @@ notmuch_config_list_destroy (notmuch_config_list_t *config_list);
 typedef enum _notmuch_config_key {
     NOTMUCH_CONFIG_FIRST,
     NOTMUCH_CONFIG_DATABASE_PATH = NOTMUCH_CONFIG_FIRST,
+    NOTMUCH_CONFIG_MAIL_ROOT,
     NOTMUCH_CONFIG_HOOK_DIR,
     NOTMUCH_CONFIG_EXCLUDE_TAGS,
     NOTMUCH_CONFIG_NEW_TAGS,
diff --git a/lib/open.cc b/lib/open.cc
index 3bb3e103..8fc17caf 100644
--- a/lib/open.cc
+++ b/lib/open.cc
@@ -263,6 +263,11 @@ _choose_xapian_path (void *ctx, const char *database_path, const char **xapian_p
     if (status)
 	goto DONE;
 
+    trial_path = talloc_asprintf (ctx, "%s/xapian", database_path);
+    status = _trial_open (trial_path, message_ptr);
+    if (status != NOTMUCH_STATUS_PATH_ERROR)
+	goto DONE;
+
     notmuch_path = talloc_asprintf (ctx, "%s/.notmuch", database_path);
     status = _db_dir_exists (notmuch_path, message_ptr);
     if (status)
diff --git a/test/T055-path-config.sh b/test/T055-path-config.sh
new file mode 100755
index 00000000..c6920ca9
--- /dev/null
+++ b/test/T055-path-config.sh
@@ -0,0 +1,90 @@
+#!/usr/bin/env bash
+test_description='Configuration of mail-root and database path'
+. $(dirname "$0")/test-lib.sh || exit 1
+
+backup_config () {
+    local test_name=$(basename $0 .sh)
+    cp ${NOTMUCH_CONFIG} notmuch-config-backup.${test_name}
+}
+
+restore_config () {
+    local test_name=$(basename $0 .sh)
+    export NOTMUCH_CONFIG="${TMP_DIRECTORY}/notmuch-config"
+    unset CONFIG_PATH
+    unset DATABASE_PATH
+    unset NOTMUCH_PROFILE
+    cp notmuch-config-backup.${test_name} ${NOTMUCH_CONFIG}
+}
+
+split_config () {
+    local dir
+    backup_config
+    dir="$TMP_DIRECTORY/database.$test_count"
+    rm -rf $dir
+    mkdir $dir
+    notmuch config set database.path $dir
+    notmuch config set database.mail_root $MAIL_DIR
+    DATABASE_PATH=$dir
+}
+
+
+
+for config in traditional split; do
+    # start each set of tests with a known set of messages
+    add_email_corpus
+
+    case $config in
+	traditional)
+	    backup_config
+	    ;;
+	split)
+	    split_config
+	    mv mail/.notmuch/xapian $DATABASE_PATH
+	    ;;
+    esac
+
+    test_begin_subtest "count ($config)"
+    output=$(notmuch count '*')
+    test_expect_equal "$output" '52'
+
+    test_begin_subtest "count+tag ($config)"
+    tag="tag${RANDOM}"
+    notmuch tag +$tag '*'
+    output=$(notmuch count tag:$tag)
+    notmuch tag -$tag '*'
+    test_expect_equal "$output" '52'
+
+    test_begin_subtest "address ($config)"
+    notmuch address --deduplicate=no --sort=newest-first --output=sender --output=recipients path:foo >OUTPUT
+    cat <<EOF >EXPECTED
+Carl Worth <cworth@cworth.org>
+notmuch@notmuchmail.org
+EOF
+    test_expect_equal_file EXPECTED OUTPUT
+
+    test_begin_subtest "dump ($config)"
+    notmuch dump is:attachment and is:signed | sort > OUTPUT
+    cat <<EOF > EXPECTED
+#notmuch-dump batch-tag:3 config,properties,tags
++attachment +inbox +signed +unread -- id:20091118005829.GB25380@dottiness.seas.harvard.edu
++attachment +inbox +signed +unread -- id:20091118010116.GC25380@dottiness.seas.harvard.edu
+EOF
+    test_expect_equal_file EXPECTED OUTPUT
+
+    test_begin_subtest "dump + tag + restore ($config)"
+    notmuch dump '*' > EXPECTED
+    notmuch tag -inbox '*'
+    notmuch restore < EXPECTED
+    notmuch dump > OUTPUT
+    test_expect_equal_file EXPECTED OUTPUT
+
+    test_begin_subtest "reindex ($config)"
+    notmuch search --output=messages '*' > EXPECTED
+    notmuch reindex '*'
+    notmuch search --output=messages '*' > OUTPUT
+    test_expect_equal_file EXPECTED OUTPUT
+
+    restore_config
+done
+
+test_done
diff --git a/test/T590-libconfig.sh b/test/T590-libconfig.sh
index 4e510e97..5cf70987 100755
--- a/test/T590-libconfig.sh
+++ b/test/T590-libconfig.sh
@@ -364,6 +364,7 @@ EOF
 cat <<'EOF' >EXPECTED
 == stdout ==
 MAIL_DIR
+MAIL_DIR
 MAIL_DIR/.notmuch/hooks
 
 inbox;unread