diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2861231d..755801f7 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -15,6 +15,8 @@ Status of the `main` branch. Changes prior to the next official version change w
     failed `--project-from-cwd` auto-detection (#1773).
   - ProjectServer: Configure trusted hosts (local hosts only) when listening on localhost
   - SerenaDashboardTrayManager: Configure trusted hosts (local hosts only)
+  - Enclose sub-prompts in XML-like tags to make scopes explicit
+  - Allow initial project prompts and project-specific newly activated modes to use templating 
 
 * CLI:
   - Fix: `start-mcp-server` help text for `--project-from-cwd` falsely promised a fallback to the CWD, which was 
diff --git a/src/serena/agent.py b/src/serena/agent.py
index 2b70389a..b9649fcf 100644
--- a/src/serena/agent.py
+++ b/src/serena/agent.py
@@ -956,14 +956,24 @@ class SerenaAgent:
             result[tool_class.get_name_from_cls()] = new_tool_class.get_name_from_cls()
         return result
 
-    def _format_prompt(self, prompt_template: str) -> str:
+    def _format_prompt_tag(self, text: str, tag: str, tag_name_attr: str | None = None) -> str:
+        open_tag = f"<{tag}" + (f' name="{tag_name_attr}"' if tag_name_attr is not None else "") + ">"
+        close_tag = f"</{tag}>"
+        return f"{open_tag}\n{text.strip()}\n{close_tag}"
+
+    def _format_prompt(self, prompt_template: str, tag: str | None = None, tag_name_attr: str | None = None) -> str:
         template = JinjaTemplate(prompt_template)
-        return template.render(
+        text = template.render(
             available_tools=self._exposed_tools.tool_names,
             available_markers=self._exposed_tools.tool_marker_names,
             tool_names=self._prompt_tool_names_mapping,
         )
 
+        if tag is not None:
+            text = self._format_prompt_tag(text, tag=tag, tag_name_attr=tag_name_attr)
+
+        return text
+
     def create_connection_prompt(self) -> str:
         """
         Returns the bootstrap prompt to be sent at MCP connection time.
@@ -997,8 +1007,8 @@ class SerenaAgent:
         self._project_prompt_status.mark_mode_prompts_as_provided(session_id)
 
         system_prompt = self.prompt_factory.create_system_prompt(
-            context_system_prompt=self._format_prompt(self._context.prompt),
-            mode_system_prompts=[self._format_prompt(mode.prompt) for mode in relevant_modes],
+            context_system_prompt=self._format_prompt(self._context.prompt, tag="context"),
+            mode_system_prompts=[self._format_prompt(mode.prompt, tag="mode", tag_name_attr=mode.name) for mode in relevant_modes],
             available_tools=available_tools.tool_names,
             available_markers=available_markers,
             global_memories_list=global_memories_str,
@@ -1007,11 +1017,11 @@ class SerenaAgent:
 
         # provide the project activation message if it hasn't yet been provided
         if self._active_project is not None and not self._project_prompt_status.is_project_activation_message_already_provided(session_id):
-            system_prompt += "\n\n" + self.get_project_activation_message(session_id)
+            system_prompt += "\n\n" + self._format_prompt_tag(self.get_project_activation_message(session_id), tag="active-project")
         elif self._project_activation_error:
             system_prompt += f"\n\nNo project is active ({self._project_activation_error})."
 
-        return system_prompt
+        return self._format_prompt_tag(system_prompt, tag="serena")
 
     def get_project_activation_message(self, session_id: str) -> str:
         """
@@ -1031,13 +1041,13 @@ class SerenaAgent:
 
         # provide basic project information (name, location, languages, encoding)
         if proj.is_newly_created:
-            msg = f"Created and activated a new project with name '{proj.project_name}' at {proj.project_root}. "
+            msg = f"Created and activated a new project with name '{proj.project_name}' at {proj.project_root}.\n"
         else:
-            msg = f"The project with name '{proj.project_name}' at {proj.project_root} is activated."
+            msg = f"The project with name '{proj.project_name}' at {proj.project_root} is activated.\n"
         if self._language_backend == LanguageBackend.LSP:
-            languages_str = ", ".join([lang.value for lang in proj.project_config.language_servers])
-            msg += f"\nProgramming languages: {languages_str}."
-        msg += f"File encoding: {proj.project_config.encoding}."
+            language_servers_str = ", ".join([ls.value for ls in proj.project_config.language_servers])
+            msg += f"Active language servers: {language_servers_str}.\n"
+        msg += f"File encoding: {proj.project_config.encoding}.\n"
 
         # add list of memories (if memories are enabled)
         include_memories = self._active_tools.contains_tool_class(ReadMemoryTool)
@@ -1045,23 +1055,22 @@ class SerenaAgent:
             project_memories = proj.memory_manager.list_project_memories()
             if project_memories:
                 msg += (
-                    f"\n{json.dumps(project_memories.to_dict())}\n"
-                    + "Use the `read_memory` tool to read these memories later if they are relevant to the task."
+                    f"{json.dumps(project_memories.to_dict())}\n"
+                    + f"Use the `{ReadMemoryTool.get_name_from_cls()}` tool to read these memories later if they are relevant to the task.\n"
                 )
             elif self._active_tools.contains_tool_class(OnboardingTool):
-                msg += "Onboarding has not been performed yet, you should call Serena's `onboarding` tool now to set up project memories."
+                msg += f"Onboarding has not been performed yet. Ask the user whether to perform onboarding via the `{OnboardingTool.get_name_from_cls()}` tool.\n"
 
         # add prompts for modes that were dynamically activated by the project
         modes_with_prompts = self._project_prompt_status.get_modes_with_prompts_to_be_provided_for_project_activation(session_id)
         if modes_with_prompts:
-            msg += "\nNewly applicable mode instructions:"
             for mode in modes_with_prompts:
-                msg += f"\n{mode.prompt}"
+                msg += self._format_prompt(mode.prompt, tag="mode", tag_name_attr=mode.name) + "\n"
         self._project_prompt_status.mark_mode_prompts_as_provided(session_id)
 
         # add project-specific prompt
         if proj.project_config.initial_prompt:
-            msg += f"\nProject-specific instructions:\n {proj.project_config.initial_prompt}"
+            msg += "\n" + self._format_prompt(proj.project_config.initial_prompt, tag="project-instructions")
 
         self._project_prompt_status.mark_project_activation_message_as_provided(session_id)
 
diff --git a/src/serena/resources/config/prompt_templates/system_prompt.yml b/src/serena/resources/config/prompt_templates/system_prompt.yml
index 78a7ad18..99604bf1 100644
--- a/src/serena/resources/config/prompt_templates/system_prompt.yml
+++ b/src/serena/resources/config/prompt_templates/system_prompt.yml
@@ -49,10 +49,8 @@ prompts:
     The context and modes of operation are described below. These determine how to interact with your user
     and which kinds of interactions are expected of you.
 
-    Context description:
     {{ context_system_prompt }}
 
-    Modes descriptions:
     {% for prompt in mode_system_prompts %}
     {{ prompt }}
     {% endfor %}