diff --git a/pyproject.toml b/pyproject.toml
index 32d8580..cacbaa3 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [project]
 name = "ohbin"
-version = "0.1.0"
+version = "0.1.1"
 description = "Declarative GitHub-release binaries for uv projects — declare a tool in pyproject, `ohbin run <tool>` downloads, SHA256-verifies, caches, and execs it. POSIX only (uses flock)."
 readme = "README.md"
 authors = [
diff --git a/src/ohbin/_add.py b/src/ohbin/_add.py
index 3b19202..914ed72 100644
--- a/src/ohbin/_add.py
+++ b/src/ohbin/_add.py
@@ -4,6 +4,7 @@
 
 import sys
 from pathlib import Path
+from typing import TYPE_CHECKING
 
 from ohbin._engine import sha256_of_url
 from ohbin._github import Asset, fetch_release
@@ -16,6 +17,13 @@
 )
 from ohbin._types import AssetEntry, ToolConfig
 
+if TYPE_CHECKING:
+    from tomlkit.items import Item, Key, Table
+
+    # One element of a tomlkit container body: a real key + item, or (None, item)
+    # for standalone whitespace/comment lines.
+    BodyEntry = tuple[Key | None, Item]
+
 # Asset filenames that are never the binary we want.
 _DENY_SUFFIXES = (
     ".txt",
@@ -125,6 +133,40 @@ def resolve_tool(*, repo: str, version: str | None, binary: str | None) -> ToolC
     )
 
 
+def _deepest_last_table(table: Table) -> Table:
+    """Descend through the last sub-table at each level to the innermost one.
+
+    Standalone comments/blank lines between the end of a tool's last sub-table and
+    the next section header are parsed by tomlkit into *that* innermost sub-table's
+    body — so this is where trailing trivia lives and must be re-attached.
+    """
+    from tomlkit.items import Table
+
+    last_sub: Table | None = None
+    for _key, item in table.value.body:
+        if isinstance(item, Table):
+            last_sub = item
+    if last_sub is None:
+        return table
+    return _deepest_last_table(last_sub)
+
+
+def _detach_trailing_trivia(table: Table) -> list[BodyEntry]:
+    """Pop the trailing run of standalone whitespace/comments from a tool's last table.
+
+    Returns them in document order; an empty list when the table ends on a real key.
+    These belong to the *following* section (a comment block before the next header),
+    not the tool — overwriting the tool entry must not eat them.
+    """
+    from tomlkit.items import Comment, Whitespace
+
+    body = _deepest_last_table(table).value.body
+    trailing: list[BodyEntry] = []
+    while body and body[-1][0] is None and isinstance(body[-1][1], (Whitespace, Comment)):
+        trailing.insert(0, body.pop())
+    return trailing
+
+
 def write_tool(pyproject: Path, name: str, cfg: ToolConfig) -> None:
     """Write/overwrite `[tool.ohbin.tools.<name>]`, preserving the rest of the file."""
     import tomlkit
@@ -147,6 +189,11 @@ def ensure(parent: TOMLDocument | Table, key: str, *, super_table: bool) -> Tabl
         super_table=True,
     )
 
+    # A comment block before the next section is parsed into the old entry's
+    # innermost body; capture it so the rebuilt entry doesn't drop it.
+    old_entry = tools.get(name)
+    trailing = _detach_trailing_trivia(old_entry) if isinstance(old_entry, Table) else []
+
     entry = tomlkit.table()
     entry["repo"] = cfg["repo"]
     entry["version"] = cfg["version"]
@@ -161,6 +208,8 @@ def ensure(parent: TOMLDocument | Table, key: str, *, super_table: bool) -> Tabl
     entry["assets"] = assets
 
     tools[name] = entry
+    if trailing:
+        _deepest_last_table(entry).value.body.extend(trailing)
     pyproject.write_text(tomlkit.dumps(doc))
 
 
diff --git a/tests/test_add.py b/tests/test_add.py
new file mode 100644
index 0000000..5ab65ae
--- /dev/null
+++ b/tests/test_add.py
@@ -0,0 +1,100 @@
+"""`write_tool`: round-trip rewrites that must not clobber surrounding file content."""
+
+from __future__ import annotations
+
+from pathlib import Path
+
+import pytest
+
+from ohbin._add import write_tool
+from ohbin._manifest import load_tool
+from ohbin._types import AssetEntry, ToolConfig
+
+
+def _cfg(version: str) -> ToolConfig:
+    return ToolConfig(
+        repo="owner/foo",
+        version=version,
+        binary="foo",
+        assets={
+            "linux-x86_64": AssetEntry(url=f"https://example/v{version}/foo-linux.tar.gz", sha256="aaaa"),
+            "darwin-arm64": AssetEntry(url=f"https://example/v{version}/foo-darwin.tar.gz", sha256="bbbb"),
+        },
+    )
+
+
+def test_overwrite_preserves_following_comment_block(tmp_path: Path) -> None:
+    # The comment block + blank line before the NEXT section is parsed by tomlkit
+    # into the tool's innermost sub-table body. Overwriting the tool must not eat it.
+    pp = tmp_path / "pyproject.toml"
+    pp.write_text(
+        "[tool.ohbin.tools.foo]\n"
+        'repo = "owner/foo"\n'
+        'version = "0.7.0"\n'
+        'binary = "foo"\n'
+        "\n"
+        "[tool.ohbin.tools.foo.assets.darwin-arm64]\n"
+        'url = "https://example/v0.7.0/foo-darwin.tar.gz"\n'
+        'sha256 = "old"\n'
+        "\n"
+        "# Single source of truth for the harness path scope.\n"
+        "# This block belongs to [tool.other], not to foo.\n"
+        "[tool.other]\n"
+        'key = "value"\n'
+    )
+
+    write_tool(pp, "foo", _cfg("0.7.5"))
+    out = pp.read_text()
+
+    assert "# Single source of truth for the harness path scope." in out
+    assert "# This block belongs to [tool.other], not to foo." in out
+    # Blank-line separator between the tool block and the comment survives.
+    assert "\n\n# Single source of truth" in out
+    # The next section header is intact and still preceded by its comments.
+    assert out.index("# This block belongs") < out.index("[tool.other]")
+    # The version bump actually happened.
+    assert load_tool("foo", pyproject=pp)["version"] == "0.7.5"
+    assert "0.7.0" not in out
+
+
+def test_add_new_tool_appends_without_touching_existing(tmp_path: Path) -> None:
+    pp = tmp_path / "pyproject.toml"
+    pp.write_text('[project]\nname = "demo"\n\n# trailing project comment\n')
+
+    write_tool(pp, "foo", _cfg("1.0.0"))
+    out = pp.read_text()
+
+    assert "# trailing project comment" in out
+    tool = load_tool("foo", pyproject=pp)
+    assert tool["version"] == "1.0.0"
+    assert set(tool["assets"]) == {"linux-x86_64", "darwin-arm64"}
+
+
+def test_overwrite_at_eof_is_idempotent_on_layout(tmp_path: Path) -> None:
+    # No following section: a re-add must produce stable, parseable output.
+    pp = tmp_path / "pyproject.toml"
+    pp.write_text("")
+    write_tool(pp, "foo", _cfg("0.1.0"))
+    write_tool(pp, "foo", _cfg("0.2.0"))
+
+    tool = load_tool("foo", pyproject=pp)
+    assert tool["version"] == "0.2.0"
+    assert "0.1.0" not in pp.read_text()
+
+
+def test_write_new_tool_into_empty_file(tmp_path: Path) -> None:
+    pp = tmp_path / "pyproject.toml"
+    pp.write_text("")
+    write_tool(pp, "foo", _cfg("3.1.4"))
+    assert load_tool("foo", pyproject=pp)["version"] == "3.1.4"
+
+
+@pytest.mark.parametrize("trailing", ["", "\n", "\n\n"])
+def test_overwrite_tolerates_varied_trailing_whitespace(tmp_path: Path, trailing: str) -> None:
+    pp = tmp_path / "pyproject.toml"
+    pp.write_text("")
+    write_tool(pp, "foo", _cfg("0.1.0"))
+    pp.write_text(pp.read_text().rstrip("\n") + trailing)
+
+    write_tool(pp, "foo", _cfg("0.2.0"))
+    assert load_tool("foo", pyproject=pp)["version"] == "0.2.0"
diff --git a/uv.lock b/uv.lock
index 52dc925..f2ed040 100644
--- a/uv.lock
+++ b/uv.lock
@@ -31,7 +31,7 @@ wheels = [
 
 [[package]]
 name = "ohbin"
-version = "0.1.0"
+version = "0.1.1"
 source = { editable = "." }
 dependencies = [
     { name = "tomlkit" },