diff --git a/README.md b/README.md
index ca0719c5b..05df7a1e4 100644
--- a/README.md
+++ b/README.md
@@ -273,10 +273,6 @@ Consistent syntax highlighting.
 require'nvim-treesitter.configs'.setup {
   highlight = {
     enable = true,
-    custom_captures = {
-      -- Highlight the @foo.bar capture group with the "Identifier" highlight group.
-      ["foo.bar"] = "Identifier",
-    },
     -- Setting this to true will run `:h syntax` and tree-sitter at the same time.
     -- Set this to `true` if you depend on 'syntax' being enabled (like for indentation).
     -- Using this option may slow down your editor, and you may see some duplicate highlights.
@@ -286,6 +282,17 @@ require'nvim-treesitter.configs'.setup {
 }
 ```
 
+You can add custom highlight captures with:
+
+```vim
+lua <<EOF
+  require"nvim-treesitter.highlight".set_custom_captures {
+    -- Highlight the @foo.bar capture group with the "Identifier" highlight group.
+    ["foo.bar"] = "Identifier",
+  }
+EOF
+```
+
 #### Incremental selection
 
 Incremental selection based on the named nodes from the grammar.
diff --git a/doc/nvim-treesitter.txt b/doc/nvim-treesitter.txt
index f3f03bfe8..e7f7932cf 100644
--- a/doc/nvim-treesitter.txt
+++ b/doc/nvim-treesitter.txt
@@ -71,7 +71,6 @@ MODULES                                              *nvim-treesitter-modules*
 
 |nvim-treesitter| provides several functionalities via modules (and submodules),
 each module makes use of the query files defined for each language,
-you can add your own queries too, see |nvim-treesitter-query-extensions|.
 
 All modules are disabled by default, and some provide default keymaps.
 Each module corresponds to an entry in the dictionary passed to the
@@ -133,8 +132,6 @@ Supported options:
 
 - enable: `true` or `false`.
 - disable: list of languages.
-- custom_captures: A map of user defined capture groups to highlight groups.
-  See |nvim-treesitter-query-extensions|.
 - additional_vim_regex_highlighting: `true` or `false`, or a list of languages.
   Set this to `true` if you depend on 'syntax' being enabled
   (like for indentation). Using this option may slow down your editor,
@@ -154,6 +151,16 @@ Supported options:
     },
   }
 <
+
+You can also set custom highlight captures
+>
+  lua <<EOF
+    require"nvim-treesitter.highlight".set_custom_captures {
+      -- Highlight the @foo.bar capture group with the "Identifier" highlight group.
+      ["foo.bar"] = "Identifier",
+    }
+  EOF
+<
 Note: The api is not stable yet.
 
 ------------------------------------------------------------------------------
diff --git a/lua/nvim-treesitter/configs.lua b/lua/nvim-treesitter/configs.lua
index 8f0f885a1..7e6b0a7b9 100644
--- a/lua/nvim-treesitter/configs.lua
+++ b/lua/nvim-treesitter/configs.lua
@@ -22,8 +22,9 @@ local is_initialized = false
 local builtin_modules = {
   highlight = {
     module_path = "nvim-treesitter.highlight",
-    enable = false,
+    -- @deprecated: use `highlight.set_custom_captures` instead
     custom_captures = {},
+    enable = false,
     is_supported = function(lang)
       return queries.has_highlights(lang)
     end,
diff --git a/lua/nvim-treesitter/highlight.lua b/lua/nvim-treesitter/highlight.lua
index ce7cf8117..b71a64eec 100644
--- a/lua/nvim-treesitter/highlight.lua
+++ b/lua/nvim-treesitter/highlight.lua
@@ -114,10 +114,6 @@ local function enable_syntax(bufnr)
   api.nvim_buf_set_option(bufnr, "syntax", "ON")
 end
 
-function M.get_config()
-  return configs.get_module "highlight"
-end
-
 function M.stop(bufnr)
   if ts.highlighter.active[bufnr] then
     ts.highlighter.active[bufnr]:destroy()
@@ -126,18 +122,13 @@ end
 
 function M.start(bufnr, lang)
   local parser = parsers.get_parser(bufnr, lang)
-  local config = M.get_config()
-
-  for k, v in pairs(config.custom_captures) do
-    hlmap[k] = v
-  end
-
   ts.highlighter.new(parser, {})
 end
 
 function M.attach(bufnr, lang)
+  local config = configs.get_module "highlight"
   M.start(bufnr, lang)
-  if should_enable_vim_regex(M.get_config(), lang) then
+  if should_enable_vim_regex(config, lang) then
     enable_syntax(bufnr)
   end
 end
@@ -147,4 +138,10 @@ function M.detach(bufnr)
   enable_syntax(bufnr)
 end
 
+function M.set_custom_captures(captures)
+  for k, v in pairs(captures) do
+    hlmap[k] = v
+  end
+end
+
 return M