diff --git a/lua/codecompanion/strategies/chat/init.lua b/lua/codecompanion/strategies/chat/init.lua
index 203fe2aa..b1941d8f 100644
--- a/lua/codecompanion/strategies/chat/init.lua
+++ b/lua/codecompanion/strategies/chat/init.lua
@@ -635,8 +635,10 @@ function Chat:submit(opts)
   message = self.References:clear(self.messages[#self.messages])
 
   self:apply_tools_and_variables(message)
+  self:check_references()
 
-  -- Check if the user has manually overriden the adapter
+  -- Check if the user has manually overriden the adapter. This is useful if the
+  -- user loses their internet connection and wants to switch to a local LLM
   if vim.g.codecompanion_adapter and self.adapter.name ~= vim.g.codecompanion_adapter then
     self.adapter = adapters.resolve(config.adapters[vim.g.codecompanion_adapter])
   end
@@ -695,11 +697,11 @@ function Chat:done()
   end
 
   self:add_message({ role = config.constants.LLM_ROLE, content = buf_parse_message(self.bufnr).content })
-
   self:add_buf_message({ role = config.constants.USER_ROLE, content = "" })
-  self.References:render()
   self.ui:display_tokens()
 
+  self.References:render()
+
   if self.status == CONSTANTS.STATUS_SUCCESS and self:has_tools() then
     buf_parse_tools(self)
   end
@@ -725,6 +727,50 @@ function Chat:done()
   end
 end
 
+---Reconcile the references table to the references in the chat buffer
+---This allows users to manually remove references themselves
+---@return nil
+function Chat:check_references()
+  local refs = self.References:get_from_chat()
+  if vim.tbl_isempty(refs) and vim.tbl_isempty(self.refs) then
+    return
+  end
+
+  -- Fetch references that exist on the chat object but not in the buffer
+  local to_remove = vim
+    .iter(pairs(self.refs))
+    :filter(function(ref, _)
+      return not vim.tbl_contains(refs, ref)
+    end)
+    :map(function(ref, _)
+      return ref
+    end)
+    :totable()
+
+  if vim.tbl_isempty(to_remove) then
+    return
+  end
+
+  -- Remove them from the messages table
+  self.messages = vim
+    .iter(self.messages)
+    :filter(function(msg)
+      if msg.opts and msg.opts.reference and vim.tbl_contains(to_remove, msg.opts.reference) then
+        return false
+      end
+      return true
+    end)
+    :totable()
+
+  -- And from the refs table
+  self.refs = vim
+    .iter(self.refs)
+    :filter(function(ref)
+      return not vim.tbl_contains(to_remove, ref)
+    end)
+    :totable()
+end
+
 ---Regenerate the response from the LLM
 ---@return nil
 function Chat:regenerate()
@@ -739,6 +785,7 @@ end
 ---@return nil
 function Chat:stop()
   local job
+  self.status = CONSTANTS.STATUS_CANCELLING
   if self.current_tool then
     job = self.current_tool
     self.current_tool = nil
diff --git a/lua/codecompanion/strategies/chat/references.lua b/lua/codecompanion/strategies/chat/references.lua
index 5c2144f6..6e23c54a 100644
--- a/lua/codecompanion/strategies/chat/references.lua
+++ b/lua/codecompanion/strategies/chat/references.lua
@@ -106,7 +106,14 @@ function References:add(ref)
   end
 
   if ref then
-    table.insert(self.chat.refs, ref)
+    self.chat.refs[ref.id] = {
+      id = ref.id,
+      name = ref.name,
+      source = ref.source,
+      opts = ref.opts or {
+        pinned = false,
+      },
+    }
   end
 
   local parsed_buffer = ts_parse_buffer(self.chat)
@@ -193,8 +200,16 @@ function References:render()
     local lines = {}
     table.insert(lines, "> Sharing:")
 
-    for _, ref in ipairs(self.chat.refs) do
-      table.insert(lines, string.format("> - %s", ref.id))
+    for ref, _ in pairs(self.chat.refs) do
+      if not ref then
+        goto continue
+      end
+      if ref.opts and ref.opts.pinned then
+        table.insert(lines, string.format("> - %s%s", config.display.chat.icons.pinned_buffer, ref))
+      else
+        table.insert(lines, string.format("> - %s", ref))
+      end
+      ::continue::
     end
     table.insert(lines, "")
 
@@ -212,4 +227,51 @@ function References:make_id_from_buf(bufnr)
   return vim.fn.fnamemodify(bufname, ":.")
 end
 
+---Get the references from the chat buffer
+---@return table
+function References:get_from_chat()
+  local refs = {}
+
+  local parser = vim.treesitter.get_parser(self.chat.bufnr, "markdown")
+  local query = vim.treesitter.query.parse(
+    "markdown",
+    string.format(
+      [[(
+  (section
+    (atx_heading) @heading
+    (#match? @heading "## %s")
+  )
+)]],
+      user_role
+    )
+  )
+
+  local root = parser:parse()[1]:root()
+  local last_heading = nil
+
+  -- Get the last heading
+  for id, node in query:iter_captures(root, self.chat.bufnr, 0, -1) do
+    if query.captures[id] == "heading" then
+      last_heading = node
+    end
+  end
+
+  if last_heading then
+    local start_row, _, _, _ = last_heading:range()
+
+    -- Get the references
+    local refs_query = vim.treesitter.query.parse("markdown", [[(block_quote (list (list_item (paragraph)? @ref)))]])
+
+    for id, node in refs_query:iter_captures(root, self.chat.bufnr, start_row, -1) do
+      if refs_query.captures[id] == "ref" then
+        local ref = vim.treesitter.get_node_text(node, self.chat.bufnr)
+        ref:gsub("^> %- ", "")
+        table.insert(refs, vim.trim(ref))
+      end
+    end
+  end
+
+  return refs
+end
+
 return References
diff --git a/lua/codecompanion/types.lua b/lua/codecompanion/types.lua
index 8a82c377..c9f2c525 100644
--- a/lua/codecompanion/types.lua
+++ b/lua/codecompanion/types.lua
@@ -72,9 +72,9 @@
 ---@field tokens? table Total tokens spent in the chat buffer so far
 
 ---@class CodeCompanion.Chat.Ref
----@field source string The source of the reference e.g. slash_command
----@field name string The name of the source e.g. buffer
 ---@field id string The unique ID of the reference which links it to a message in the chat buffer and is displayed to the user
+---@field name string The name of the source e.g. buffer
+---@field source string The source of the reference e.g. slash_command
 ---@field opts? table
 
 ---@class CodeCompanion.Chat.UI
diff --git a/tests/strategies/chat/test_references.lua b/tests/strategies/chat/test_references.lua
index 8f740474..6b3ba84b 100644
--- a/tests/strategies/chat/test_references.lua
+++ b/tests/strategies/chat/test_references.lua
@@ -7,7 +7,7 @@ local chat
 
 T["References"] = new_set({
   hooks = {
-    pre_once = function()
+    pre_case = function()
       chat, _ = h.setup_chat_buffer()
     end,
     post_once = function()
@@ -36,4 +36,54 @@ T["References"]["Can be added to the UI of the chat buffer"] = function()
   h.eq("> - testing again", buffer[5])
 end
 
+T["References"]["Can be deleted"] = function()
+  -- First add a reference and a message that uses it
+  chat.References:add({
+    source = "test",
+    name = "test",
+    id = "<buf>test.lua</buf>",
+  })
+
+  -- Add messages with and without references
+  chat.messages = {
+    {
+      role = "user",
+      content = "Message with reference",
+      opts = {
+        reference = "<buf>test.lua</buf>",
+      },
+    },
+    {
+      role = "user",
+      content = "Message without reference",
+      opts = {},
+    },
+  }
+
+  -- Store initial message count
+  local initial_count = #chat.messages
+  h.eq(initial_count, 2, "Should start with 2 messages")
+  h.eq(vim.tbl_count(chat.refs), 1, "Should have 1 reference")
+
+  -- Mock the get_from_chat method to return empty refs
+  chat.References.get_from_chat = function()
+    return {}
+  end
+
+  -- Run the check_references function
+  chat:check_references()
+
+  -- Verify results
+  h.eq(#chat.messages, 1, "Should have 1 message after reference removal")
+  h.eq(chat.messages[1].content, "Message without reference", "Message without reference should remain")
+  h.eq(vim.tbl_count(chat.refs), 0, "Should have 0 references")
+
+  -- Verify the message with reference was removed
+  local has_ref_message = vim.iter(chat.messages):any(function(msg)
+    return msg.opts.reference == "<buf>test.lua</buf>"
+  end)
+
+  h.eq(has_ref_message, false, "Message with removed reference should be gone")
+end
+
 return T