diff --git a/test/test_alt.py b/test/test_alt.py
index ef421f7..138d609 100644
--- a/test/test_alt.py
+++ b/test/test_alt.py
@@ -217,6 +217,29 @@ def test_auto_alt(runner, yadm_cmd, paths, autoalt):
                 assert str(paths.work.join(source_file)) not in linked
 
 
+@pytest.mark.usefixtures("ds1_copy")
+@pytest.mark.parametrize("autoexclude", [None, "true", "false"])
+def test_alt_exclude(runner, yadm_cmd, paths, autoexclude):
+    """Test alt exclude"""
+
+    # set the value of auto-exclude
+    if autoexclude:
+        os.system(" ".join(yadm_cmd("config", "yadm.auto-exclude", autoexclude)))
+
+    utils.create_alt_files(paths, "##default")
+    run = runner(yadm_cmd("alt", "-d"))
+    assert run.success
+
+    run = runner(yadm_cmd("status", "-z", "-uall", "--ignored"))
+    assert run.success
+    assert run.err == ""
+    status = run.out.split("\0")
+
+    for link_path in TEST_PATHS:
+        flags = "??" if autoexclude == "false" else "!!"
+        assert f"{flags} {link_path}" in status
+
+
 @pytest.mark.usefixtures("ds1_copy")
 def test_stale_link_removal(runner, yadm_cmd, paths):
     """Stale links to alternative files are removed
diff --git a/test/test_unit_exclude_encrypted.py b/test/test_unit_exclude_encrypted.py
index bbe29fd..1daa891 100644
--- a/test/test_unit_exclude_encrypted.py
+++ b/test/test_unit_exclude_encrypted.py
@@ -9,7 +9,12 @@ import pytest
 def test_exclude_encrypted(runner, tmpdir, yadm, encrypt_exists, auto_exclude, exclude):
     """Test exclude_encrypted()"""
 
-    header = "# yadm-auto-excludes\n# This section is managed by yadm.\n# Any edits below will be lost.\n"
+    header = """\
+# yadm-auto-excludes
+# This section is managed by yadm.
+# Any edits below will be lost.
+# yadm encrypt
+"""
 
     config_function = 'function config() { echo "false";}'
     if auto_exclude:
diff --git a/yadm b/yadm
index 2dbb540..2e8bea2 100755
--- a/yadm
+++ b/yadm
@@ -691,6 +691,11 @@ function set_local_alt_values() {
 }
 
 function alt_linking() {
+  local -a exclude=()
+
+  local log="debug"
+  [ -n "$loud" ] && log="echo"
+
   local -i index
   for ((index = 0; index < ${#alt_targets[@]}; ++index)); do
     local target="${alt_targets[$index]}"
@@ -709,17 +714,17 @@ function alt_linking() {
     if [[ -n "$template_processor" ]]; then
       template "$template_processor" "$source" "$target"
     elif [[ "$do_copy" -eq 1 ]]; then
-      debug "Copying $source to $target"
-      [[ -n "$loud" ]] && echo "Copying $source to $target"
-
+      $log "Copying $source to $target"
       cp -f "$source" "$target"
     else
-      debug "Linking $source to $target"
-      [[ -n "$loud" ]] && echo "Linking $source to $target"
-
+      $log "Linking $source to $target"
       ln_relative "$source" "$target"
     fi
+
+    exclude+=("${target#"$YADM_WORK"}")
   done
+
+  update_exclude alt "${exclude[@]}"
 }
 
 function ln_relative() {
@@ -1473,18 +1478,35 @@ function version() {
 
 # ****** Utility Functions ******
 
-function exclude_encrypted() {
+function update_exclude() {
 
   local auto_exclude
   auto_exclude=$(config --bool yadm.auto-exclude)
   [ "$auto_exclude" == "false" ] && return 0
 
-  # do nothing if there is no YADM_ENCRYPT
-  [ -e "$YADM_ENCRYPT" ] || return 0
+  local exclude_path="${YADM_REPO}/info/exclude"
+  local newline=$'\n'
 
-  readonly exclude_path="${YADM_REPO}/info/exclude"
-  readonly newline=$'\n'
-  readonly exclude_flag="# yadm-auto-excludes"
+  local part_path="$exclude_path.yadm-$1"
+  local part_str
+  part_str=$(join_string "$newline" "${@:2}")
+
+  if [ -e "$part_path" ]; then
+    if [ "$part_str" = "$(<"$part_path")" ]; then
+      return
+    fi
+
+    rm -f "$part_path"
+  elif [ -z "$part_str" ]; then
+    return
+  fi
+
+  if [ -n "$part_str" ]; then
+    assert_parent "$part_path"
+    cat >"$part_path" <<<"$part_str"
+  fi
+
+  local exclude_flag="# yadm-auto-excludes"
 
   local exclude_header="${exclude_flag}${newline}"
   exclude_header="${exclude_header}# This section is managed by yadm."
@@ -1492,30 +1514,6 @@ function exclude_encrypted() {
   exclude_header="${exclude_header}# Any edits below will be lost."
   exclude_header="${exclude_header}${newline}"
 
-  # read encrypt
-  local encrypt_data=""
-  local pattern
-  while IFS='' read -r pattern || [ -n "$pattern" ]; do
-    case ${pattern:0:1} in
-      \#)
-        pattern=""
-        ;;
-      !)
-        # Prepend / to the pattern so that it matches the same files as in
-        # parse_encrypt (i.e. only from the root)
-        pattern="!/${pattern:1}$newline"
-        ;;
-      *)
-        if ! [[ $pattern =~ ^[[:blank:]]*(#|$) ]]; then
-          pattern="/$pattern$newline"
-        else
-          pattern=""
-        fi
-        ;;
-    esac
-    encrypt_data="${encrypt_data}${pattern}"
-  done <"$YADM_ENCRYPT"
-
   # read info/exclude
   local unmanaged=""
   local managed=""
@@ -1532,14 +1530,39 @@ function exclude_encrypted() {
     done <"$exclude_path"
   fi
 
-  if [ "${exclude_header}${encrypt_data}" != "$managed" ]; then
+  local exclude_str=""
+  for suffix in alt encrypt; do
+    if [ -e "${exclude_path}.yadm-$suffix" ]; then
+      local header="# yadm $suffix$newline"
+      exclude_str="$exclude_str$header$(<"$exclude_path".yadm-"$suffix")"
+    fi
+  done
+
+  if [ "${exclude_header}${exclude_str}${newline}" != "$managed" ]; then
     debug "Updating ${exclude_path}"
-    assert_parent "$exclude_path"
-    printf "%s" "${unmanaged}${exclude_header}${encrypt_data}" >"$exclude_path"
+    cat >"$exclude_path" <<<"${unmanaged}${exclude_header}${exclude_str}"
   fi
 
   return 0
+}
 
+function exclude_encrypted() {
+  local -a exclude=()
+
+  if [ -r "$YADM_ENCRYPT" ]; then
+    local pattern
+    while IFS='' read -r pattern || [ -n "$pattern" ]; do
+      # Prepend / to the pattern so that it matches the same files as in
+      # parse_encrypt (i.e. only from the root)
+      if [ "${pattern:0:1}" = "!" ]; then
+        exclude+=("!/${pattern:1}")
+      elif ! [[ $pattern =~ ^[[:blank:]]*(#|$) ]]; then
+        exclude+=("/$pattern")
+      fi
+    done <"$YADM_ENCRYPT"
+  fi
+
+  update_exclude encrypt "${exclude[@]}"
 }
 
 function query_distro() {
@@ -1956,19 +1979,11 @@ function parse_encrypt() {
 
   local pattern
   while IFS='' read -r pattern || [ -n "$pattern" ]; do
-    case ${pattern:0:1} in
-      \#)
-        # Ignore comments
-        ;;
-      !)
-        exclude+=("--exclude=/${pattern:1}")
-        ;;
-      *)
-        if ! [[ $pattern =~ ^[[:blank:]]*(#|$) ]]; then
-          include+=("$pattern")
-        fi
-        ;;
-    esac
+    if [ "${pattern:0:1}" = "!" ]; then
+      exclude+=("--exclude=/${pattern:1}")
+    elif ! [[ $pattern =~ ^[[:blank:]]*(#|$) ]]; then
+      include+=("$pattern")
+    fi
   done <"$YADM_ENCRYPT"
 
   if [ ${#include[@]} -gt 0 ]; then
diff --git a/yadm.1 b/yadm.1
index caa37de..52ef994 100644
--- a/yadm.1
+++ b/yadm.1
@@ -363,7 +363,8 @@ you may still run "yadm alt" manually to create the alternate links. This
 feature is enabled by default.
 .TP
 .B yadm.auto-exclude
-Disable the automatic exclusion of patterns defined in
+Disable the automatic exclusion of created alternate links, template files and
+patterns defined in
 .IR $HOME/.config/yadm/encrypt .
 This feature is enabled by default.
 .TP
@@ -614,6 +615,12 @@ configuration.
 Even if disabled, links can be manually created by running
 .BR "yadm alt" .
 
+Created links are automatically added to the repository's
+.I info/exclude
+file. This can be disabled using the
+.I yadm.auto-exclude
+configuration.
+
 Class is a special value which is stored locally on each host (inside the local
 repository). To use alternate symlinks using class, you must set the value of
 class using the configuration
@@ -748,6 +755,12 @@ would look like:
   <%+ whatever.extra %>
   <% fi -%>
 
+Created files are automatically added to the repository's
+.I info/exclude
+file. This can be disabled using the
+.I yadm.auto-exclude
+configuration.
+
 .SH ENCRYPTION
 
 It can be useful to manage confidential files, like SSH or GPG keys, across