diff --git a/DESCRIPTION b/DESCRIPTION
index 36ce49b8..1a8c7c62 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -32,8 +32,9 @@ Imports:
     utils,
     xfun,
     yaml (>= 2.3.10)
-Suggests: 
-    bslib,
+Suggests:
+    brand.yml,
+    bslib (>= 0.9.0),
     callr,
     curl,
     dplyr,
diff --git a/R/list.R b/R/list.R
index 597ef8ef..9b796748 100644
--- a/R/list.R
+++ b/R/list.R
@@ -19,6 +19,10 @@ quarto_list_extensions <- function() {
   x <- quarto_list(args, quarto_bin = quarto_bin, echo = FALSE)
   # Clean the stderr output to remove extra spaces and ensure consistent formatting
   stderr_cleaned <- gsub("\\s+$", "", x$stderr)
+  # Quarto CLI prepends a "Quarto version: X.Y.Z" line to stderr when log level
+  # is DEBUG (auto-enabled in GHA debug mode). Strip it so read.table() can use
+  # the real header row. See https://github.com/quarto-dev/quarto-cli/issues/14532.
+  stderr_cleaned <- sub("^Quarto version:[^\n]*\n", "", stderr_cleaned)
   if (grepl("No extensions are installed", stderr_cleaned)) {
     invisible()
   } else {
diff --git a/R/quarto-args.R b/R/quarto-args.R
index b3f79011..940da43c 100644
--- a/R/quarto-args.R
+++ b/R/quarto-args.R
@@ -26,3 +26,31 @@ append_cli_args <- function(new, append_to = NULL, after = length(append_to)) {
   }
   new
 }
+
+cli_arg_metadata <- function(metadata = NULL, metadata_file = NULL) {
+  if (is.null(metadata) && is.null(metadata_file)) {
+    return(list(args = character(), tmp_file = NULL))
+  }
+  if (is.null(metadata)) {
+    return(list(
+      args = c("--metadata-file", metadata_file),
+      tmp_file = NULL
+    ))
+  }
+  if (!is.null(metadata_file)) {
+    file_content <- yaml::read_yaml(metadata_file, eval.expr = FALSE)
+    metadata <- merge_list(file_content, metadata)
+  }
+  tmp <- tempfile(pattern = "quarto-meta", fileext = ".yml")
+  # Remove tmp if write_yaml() errors before we hand the path to the
+  # caller; the caller (e.g. quarto_render()) registers its own
+  # on.exit cleanup for the success path.
+  success <- FALSE
+  on.exit(if (!success) unlink(tmp), add = TRUE)
+  write_yaml(metadata, tmp)
+  success <- TRUE
+  list(
+    args = c("--metadata-file", tmp),
+    tmp_file = tmp
+  )
+}
diff --git a/R/remove.R b/R/remove.R
index 7dd68a0a..928fe344 100644
--- a/R/remove.R
+++ b/R/remove.R
@@ -28,9 +28,23 @@ quarto_remove_extension <- function(
   rlang::check_required(extension)
 
   installed_extensions <- quarto_list_extensions()
-  if (is.null(installed_extensions)) {
+  # TODO: adapt based on https://github.com/quarto-dev/quarto-r/issues/301
+  if (quarto_available(max = "1.9")) {
+    if (is.null(installed_extensions)) {
+      if (!quiet) {
+        cli::cli_alert_warning("No extensions installed.")
+      }
+      return(invisible(FALSE))
+    }
+  }
+
+  # Check extension is installed
+  is_installed <- extension %in% installed_extensions$Id
+  if (!is_installed) {
     if (!quiet) {
-      cli::cli_alert_warning("No extensions installed.")
+      cli::cli_alert_warning(
+        "{.str {extension}} is not among installed extensions."
+      )
     }
     return(invisible(FALSE))
   }
diff --git a/R/render.R b/R/render.R
index 8c17e6bd..15f845cb 100644
--- a/R/render.R
+++ b/R/render.R
@@ -197,18 +197,10 @@ quarto_render <- function(
     args <- c(args, "--cache-refresh")
   }
   # metadata to pass to quarto render
-  if (!is.null(metadata)) {
-    # We merge meta if there is metadata_file passed
-    if (!missing(metadata_file)) {
-      file_content <- yaml::read_yaml(metadata_file, eval.expr = FALSE)
-      metadata <- merge_list(file_content, metadata)
-    }
-    meta_file <- tempfile(pattern = "quarto-meta", fileext = ".yml")
-    on.exit(unlink(meta_file), add = TRUE)
-    write_yaml(metadata, meta_file)
-    args <- c(args, "--metadata-file", meta_file)
-  } else if (!missing(metadata_file)) {
-    args <- c(args, "--metadata-file", metadata_file)
+  meta_result <- cli_arg_metadata(metadata, metadata_file)
+  args <- c(args, meta_result$args)
+  if (!is.null(meta_result$tmp_file)) {
+    on.exit(unlink(meta_result$tmp_file), add = TRUE)
   }
   if (isTRUE(debug)) {
     args <- c(args, "--debug")
diff --git a/tests/testthat/_snaps/metadata-render/metadata-toplevel-override.test.out b/tests/testthat/_snaps/metadata-render/metadata-toplevel-override.test.out
new file mode 100644
index 00000000..0983e9d0
--- /dev/null
+++ b/tests/testthat/_snaps/metadata-render/metadata-toplevel-override.test.out
@@ -0,0 +1,10 @@
+Pandoc
+  Meta
+    { unMeta =
+        fromList
+          [ ( "custom-key" , MetaInlines [ Str "overridden" ] )
+          , ( "title" , MetaInlines [ Str "Doc" ] )
+          , ( "yml-only-key" , MetaInlines [ Str "kept" ] )
+          ]
+    }
+  []
diff --git a/tests/testthat/_snaps/quarto.md b/tests/testthat/_snaps/quarto.md
index b5391a47..4b884212 100644
--- a/tests/testthat/_snaps/quarto.md
+++ b/tests/testthat/_snaps/quarto.md
@@ -8,7 +8,7 @@
       Caused by error:
       x Error returned by quarto CLI.
       i Rerun with `quiet = FALSE` to see the full error message.
-      Caused by error:
+      Caused by error in `processx::run()`:
       ! System command 'quarto' failed
 
 # quarto_run report full quarto cli error message
@@ -26,7 +26,7 @@
         Stack trace:
         <stack trace>
         
-      Caused by error:
+      Caused by error in `processx::run()`:
       ! System command 'quarto' failed
 
 # is_using_quarto correctly check directory
diff --git a/tests/testthat/_snaps/remove.md b/tests/testthat/_snaps/remove.md
index 52b77684..0d18b167 100644
--- a/tests/testthat/_snaps/remove.md
+++ b/tests/testthat/_snaps/remove.md
@@ -1,14 +1,16 @@
 # Removing an extension
 
     Code
-      expect_false(quarto_remove_extension("quarto-ext/fontawesome", no_prompt = TRUE))
+      withr::with_dir(wd, expect_false(quarto_remove_extension(
+        "quarto-ext/fontawesome", no_prompt = TRUE)))
     Message
-      ! No extensions installed.
+      ! "quarto-ext/fontawesome" is not among installed extensions.
 
 ---
 
     Code
-      expect_true(quarto_remove_extension("quarto-ext/fontawesome", no_prompt = TRUE))
+      withr::with_dir(wd, expect_true(quarto_remove_extension(
+        "quarto-ext/fontawesome", no_prompt = TRUE)))
     Message
       v Extension `quarto-ext/fontawesome` successfully removed.
 
diff --git a/tests/testthat/_snaps/render/metadata-file.test.out b/tests/testthat/_snaps/render/metadata-file.test.out
deleted file mode 100644
index 2490cc43..00000000
--- a/tests/testthat/_snaps/render/metadata-file.test.out
+++ /dev/null
@@ -1,6 +0,0 @@
-Pandoc
-  Meta
-    { unMeta =
-        fromList [ ( "title" , MetaInlines [ Str "test" ] ) ]
-    }
-  [ Para [ Str "content" ] ]
diff --git a/tests/testthat/_snaps/render/metadata-merged.test.out b/tests/testthat/_snaps/render/metadata-merged.test.out
deleted file mode 100644
index 4cb8ddd8..00000000
--- a/tests/testthat/_snaps/render/metadata-merged.test.out
+++ /dev/null
@@ -1,10 +0,0 @@
-Pandoc
-  Meta
-    { unMeta =
-        fromList
-          [ ( "any" , MetaInlines [ Str "one" ] )
-          , ( "other" , MetaInlines [ Str "thing" ] )
-          , ( "title" , MetaInlines [ Str "test2" ] )
-          ]
-    }
-  [ Para [ Str "content" ] ]
diff --git a/tests/testthat/_snaps/render/metadata.test.out b/tests/testthat/_snaps/render/metadata.test.out
deleted file mode 100644
index 2490cc43..00000000
--- a/tests/testthat/_snaps/render/metadata.test.out
+++ /dev/null
@@ -1,6 +0,0 @@
-Pandoc
-  Meta
-    { unMeta =
-        fromList [ ( "title" , MetaInlines [ Str "test" ] ) ]
-    }
-  [ Para [ Str "content" ] ]
diff --git a/tests/testthat/helpers.R b/tests/testthat/helpers.R
index 7e50a907..eda8b077 100644
--- a/tests/testthat/helpers.R
+++ b/tests/testthat/helpers.R
@@ -185,6 +185,11 @@ transform_quarto_cli_in_output <- function(
 
   return(
     function(lines) {
+      # Quarto CLI prepends "Quarto version: X.Y.Z" on stderr under DEBUG log
+      # level (auto-on in GHA debug mode). Strip so snapshots stay stable.
+      # See https://github.com/quarto-dev/quarto-cli/issues/14532.
+      lines <- lines[!grepl("^\\s*Quarto version:\\s+[0-9]", lines)]
+
       if (hide_stack) {
         # Hide possible stack first
         stack_trace_index <- which(grepl("\\s*Stack trace\\:", lines))
diff --git a/tests/testthat/test-list.R b/tests/testthat/test-list.R
index 12a8d827..c5e62892 100644
--- a/tests/testthat/test-list.R
+++ b/tests/testthat/test-list.R
@@ -5,17 +5,19 @@ test_that("Listing extensions", {
   skip_if_offline("github.com")
   qmd <- local_qmd_file(c("content"))
   withr::local_dir(dirname(qmd))
-  expect_null(quarto_list_extensions())
+  # TODO: Adapt depending on https://github.com/quarto-dev/quarto-r/issues/301
+  # expect_null(quarto_list_extensions())
+  default <- quarto_list_extensions()$Id
   quarto_add_extension("quarto-ext/fontawesome", no_prompt = TRUE, quiet = TRUE)
   expect_true(dir.exists("_extensions/quarto-ext/fontawesome"))
   expect_identical(
-    quarto_list_extensions()$Id,
+    setdiff(quarto_list_extensions()$Id, default),
     c("quarto-ext/fontawesome")
   )
   quarto_add_extension("quarto-ext/lightbox", no_prompt = TRUE, quiet = TRUE)
   expect_true(dir.exists("_extensions/quarto-ext/lightbox"))
   expect_identical(
-    quarto_list_extensions()$Id,
+    setdiff(quarto_list_extensions()$Id, default),
     c("quarto-ext/fontawesome", "quarto-ext/lightbox")
   )
 })
diff --git a/tests/testthat/test-metadata-args.R b/tests/testthat/test-metadata-args.R
new file mode 100644
index 00000000..02fad936
--- /dev/null
+++ b/tests/testthat/test-metadata-args.R
@@ -0,0 +1,110 @@
+test_that("cli_arg_metadata returns empty args when both inputs NULL", {
+  result <- cli_arg_metadata(metadata = NULL, metadata_file = NULL)
+  expect_identical(result$args, character())
+  expect_null(result$tmp_file)
+})
+
+test_that("cli_arg_metadata with metadata only writes temp YAML and uses --metadata-file", {
+  skip_if_not_installed("withr")
+  skip_if_not_installed("yaml")
+  result <- cli_arg_metadata(
+    metadata = list(title = "test", lang = "fr"),
+    metadata_file = NULL
+  )
+  withr::defer(unlink(result$tmp_file))
+
+  expect_length(result$args, 2L)
+  expect_identical(result$args[1], "--metadata-file")
+  expect_true(file.exists(result$args[2]))
+  expect_identical(result$args[2], result$tmp_file)
+
+  written <- yaml::read_yaml(result$tmp_file)
+  expect_identical(written, list(title = "test", lang = "fr"))
+})
+
+test_that("cli_arg_metadata with metadata_file only passes path verbatim", {
+  skip_if_not_installed("withr")
+  yml <- withr::local_tempfile(fileext = ".yml")
+  yaml::write_yaml(list(title = "file-title"), yml)
+
+  result <- cli_arg_metadata(metadata = NULL, metadata_file = yml)
+  expect_identical(result$args, c("--metadata-file", yml))
+  expect_null(result$tmp_file)
+})
+
+test_that("cli_arg_metadata merges metadata over metadata_file with metadata winning", {
+  skip_if_not_installed("withr")
+  skip_if_not_installed("yaml")
+  yml <- withr::local_tempfile(fileext = ".yml")
+  yaml::write_yaml(list(title = "from-file", other = "kept"), yml)
+
+  result <- cli_arg_metadata(
+    metadata = list(title = "from-list", new = "added"),
+    metadata_file = yml
+  )
+  withr::defer(unlink(result$tmp_file))
+
+  expect_identical(result$args[1], "--metadata-file")
+  expect_identical(result$args[2], result$tmp_file)
+
+  written <- yaml::read_yaml(result$tmp_file)
+  expect_identical(
+    written,
+    list(title = "from-list", other = "kept", new = "added")
+  )
+})
+
+test_that("cli_arg_metadata preserves nested list structure in temp YAML", {
+  skip_if_not_installed("withr")
+  skip_if_not_installed("yaml")
+  nested <- list(format = list(html = list(`toc-title` = "Custom")))
+  result <- cli_arg_metadata(metadata = nested, metadata_file = NULL)
+  withr::defer(unlink(result$tmp_file))
+
+  written <- yaml::read_yaml(result$tmp_file)
+  expect_identical(written, nested)
+})
+
+test_that("cli_arg_metadata removes temp file if write_yaml errors", {
+  skip_if_not_installed("withr")
+  captured_tmp <- NULL
+  local_mocked_bindings(
+    write_yaml = function(x, file) {
+      captured_tmp <<- file
+      file.create(file)
+      stop("simulated write failure")
+    }
+  )
+
+  expect_error(
+    cli_arg_metadata(metadata = list(title = "x"), metadata_file = NULL),
+    "simulated write failure"
+  )
+  expect_false(is.null(captured_tmp))
+  expect_false(file.exists(captured_tmp))
+})
+
+test_that("cli_arg_metadata merge is shallow (top-level keys replaced wholesale)", {
+  # Documents current behavior - metadata replaces top-level keys entirely.
+  # If we ever switch to deep merge, this test should be updated, not silently broken.
+  skip_if_not_installed("withr")
+  skip_if_not_installed("yaml")
+  yml <- withr::local_tempfile(fileext = ".yml")
+  yaml::write_yaml(
+    list(format = list(html = list(toc = TRUE, `toc-title` = "Original"))),
+    yml
+  )
+
+  result <- cli_arg_metadata(
+    metadata = list(format = list(html = list(`toc-title` = "Overridden"))),
+    metadata_file = yml
+  )
+  withr::defer(unlink(result$tmp_file))
+
+  written <- yaml::read_yaml(result$tmp_file)
+  # toc=TRUE from file is LOST because metadata's `format` replaces wholesale
+  expect_identical(
+    written,
+    list(format = list(html = list(`toc-title` = "Overridden")))
+  )
+})
diff --git a/tests/testthat/test-metadata-render.R b/tests/testthat/test-metadata-render.R
new file mode 100644
index 00000000..cccdb758
--- /dev/null
+++ b/tests/testthat/test-metadata-render.R
@@ -0,0 +1,80 @@
+# Integration test for the actual motivation behind switching to
+# --metadata-file in PR #52: top-level (non-format-nested) keys from
+# _quarto.yml can be overridden, which --metadata key:value cannot do
+# (--metadata only reaches keys under the chosen output format).
+# Format-nested keys (e.g. format.html.toc-title) are consumed by
+# Quarto before reaching Pandoc, so they do not appear in native AST;
+# a top-level key is the right surface to demonstrate the override.
+# A Lua filter scrubs all metadata except an allowlist so the
+# native-AST snapshot stays small and stable across Quarto versions.
+
+test_that("metadata overrides keys from _quarto.yml", {
+  skip_if_no_quarto()
+  skip_if_not_installed("withr")
+  skip_if_not_installed("xfun")
+
+  proj <- withr::local_tempdir("quarto-metadata-nested-")
+
+  xfun::write_utf8(
+    c(
+      "project:",
+      "  type: default",
+      "format:",
+      "  html:",
+      "    toc-title: Original",
+      "custom-key: from-quarto-yml",
+      # control key only set in _quarto.yml; proves project metadata
+      # was actually read (not just our --metadata-file override)
+      "yml-only-key: kept"
+    ),
+    file.path(proj, "_quarto.yml")
+  )
+
+  xfun::write_utf8(
+    c(
+      "---",
+      "title: Doc",
+      "---",
+      "",
+      "body"
+    ),
+    file.path(proj, "index.qmd")
+  )
+
+  # Lua filter: keep only allowlisted meta keys, drop document body.
+  # Result is a tiny, deterministic native AST regardless of what else
+  # Quarto injects (engines, extension paths, etc.).
+  xfun::write_utf8(
+    c(
+      'function Pandoc(doc)',
+      '  local wanted = {',
+      '    ["title"] = true,',
+      '    ["custom-key"] = true,',
+      '    ["yml-only-key"] = true,',
+      '  }',
+      '  local kept = pandoc.Meta({})',
+      '  for k, v in pairs(doc.meta) do',
+      '    if wanted[k] then kept[k] = v end',
+      '  end',
+      '  return pandoc.Pandoc({}, kept)',
+      'end'
+    ),
+    file.path(proj, "extract-meta.lua")
+  )
+
+  withr::local_dir(proj)
+
+  quarto_render(
+    "index.qmd",
+    output_format = "native",
+    metadata = list(`custom-key` = "overridden"),
+    quarto_args = c("--lua-filter", "extract-meta.lua"),
+    quiet = TRUE
+  )
+
+  announce_snapshot_file(name = "metadata-toplevel-override.test.out")
+  expect_snapshot_file(
+    file.path(proj, "index.native"),
+    "metadata-toplevel-override.test.out"
+  )
+})
diff --git a/tests/testthat/test-remove.R b/tests/testthat/test-remove.R
index 5ccb8bc8..ee3e1e6c 100644
--- a/tests/testthat/test-remove.R
+++ b/tests/testthat/test-remove.R
@@ -2,16 +2,30 @@ test_that("Removing an extension", {
   skip_if_no_quarto()
   skip_if_offline("github.com")
   qmd <- local_qmd_file(c("content"))
-  withr::local_dir(dirname(qmd))
-  expect_snapshot(expect_false(quarto_remove_extension(
-    "quarto-ext/fontawesome",
-    no_prompt = TRUE
-  )))
-  quarto_add_extension("quarto-ext/fontawesome", no_prompt = TRUE, quiet = TRUE)
-  expect_true(dir.exists("_extensions/quarto-ext/fontawesome"))
-  expect_snapshot(expect_true(quarto_remove_extension(
-    "quarto-ext/fontawesome",
-    no_prompt = TRUE
-  )))
-  expect_false(dir.exists("_extensions"))
+  # with expect_snapshot, can't use withr::local_dir()
+  wd <- dirname(qmd)
+  local_edition(3)
+  expect_snapshot(withr::with_dir(
+    wd,
+    expect_false(quarto_remove_extension(
+      "quarto-ext/fontawesome",
+      no_prompt = TRUE
+    ))
+  ))
+  withr::with_dir(wd, {
+    quarto_add_extension(
+      "quarto-ext/fontawesome",
+      no_prompt = TRUE,
+      quiet = TRUE
+    )
+    expect_true(dir.exists("_extensions/quarto-ext/fontawesome"))
+  })
+  expect_snapshot(withr::with_dir(
+    wd,
+    expect_true(quarto_remove_extension(
+      "quarto-ext/fontawesome",
+      no_prompt = TRUE
+    ))
+  ))
+  withr::with_dir(wd, expect_false(dir.exists("_extensions")))
 })
diff --git a/tests/testthat/test-render.R b/tests/testthat/test-render.R
index d0c6ca38..7bb92958 100644
--- a/tests/testthat/test-render.R
+++ b/tests/testthat/test-render.R
@@ -11,46 +11,6 @@ test_that("R Markdown documents can be rendered", {
   unlink("test.html")
 })
 
-test_that("metadata argument works in quarto_render", {
-  skip_if_no_quarto()
-  qmd <- local_qmd_file(c("content"))
-  # metadata
-  expect_snapshot_qmd_output(
-    name = "metadata",
-    input = qmd,
-    output_format = "native",
-    metadata = list(title = "test")
-  )
-})
-
-test_that("metadata-file argument works in quarto_render", {
-  skip_if_no_quarto()
-  skip_if_not_installed("withr")
-  qmd <- local_qmd_file(c("content"))
-  yaml <- withr::local_tempfile(fileext = ".yml")
-  write_yaml(list(title = "test"), yaml)
-  expect_snapshot_qmd_output(
-    name = "metadata-file",
-    input = qmd,
-    output_format = "native",
-    metadata_file = yaml
-  )
-})
-
-test_that("metadata-file and metadata are merged in quarto_render", {
-  skip_if_no_quarto()
-  skip_if_not_installed("withr")
-  qmd <- local_qmd_file(c("content"))
-  yaml <- withr::local_tempfile(fileext = ".yml")
-  write_yaml(list(title = "test", other = "thing"), yaml)
-  expect_snapshot_qmd_output(
-    name = "metadata-merged",
-    input = qmd,
-    output_format = "native",
-    metadata_file = yaml,
-    metadata = list(title = "test2", any = "one")
-  )
-})
 
 test_that("quarto_args in quarto_render", {
   skip_if_no_quarto()
diff --git a/tests/testthat/test-theme.R b/tests/testthat/test-theme.R
index 2e1ba8a0..587376b5 100644
--- a/tests/testthat/test-theme.R
+++ b/tests/testthat/test-theme.R
@@ -2,6 +2,8 @@
 skip_on_cran()
 skip_if_no_quarto()
 skip_if_not_installed("withr")
+skip_if_not_installed("brand.yml")
+skip_if_not_installed("bslib", "0.9.0")
 
 # We need to install the package in a temporary library when we are in dev mode
 install_dev_package()
diff --git a/tests/testthat/test-update.R b/tests/testthat/test-update.R
index 25263ec2..565757fd 100644
--- a/tests/testthat/test-update.R
+++ b/tests/testthat/test-update.R
@@ -8,16 +8,18 @@ test_that("Updating an extension", {
     no_prompt = TRUE,
     quiet = TRUE
   )
-  expect_equal(quarto_list_extensions()$Version, "0.0.1")
+  installed <- quarto_list_extensions()
+  fontawesome_row <- installed[installed$Id == "quarto-ext/fontawesome", ]
+  expect_equal(fontawesome_row$Version, "0.0.1")
   quarto_update_extension(
     "quarto-ext/fontawesome",
     no_prompt = TRUE,
     quiet = TRUE
   )
   expect_true(dir.exists("_extensions/quarto-ext/fontawesome"))
-  expect_true(
-    as.numeric_version(current_version <- quarto_list_extensions()$Version) >
-      "0.0.1"
-  )
+  installed <- quarto_list_extensions()
+  fontawesome_row <- installed[installed$Id == "quarto-ext/fontawesome", ]
+  current_version <- fontawesome_row$Version
+  expect_true(as.numeric_version(current_version) > "0.0.1")
   expect_false(identical(current_version, "0.0.1"))
 })
diff --git a/tests/testthat/test-utils-extract.R b/tests/testthat/test-utils-extract.R
index 4ffd3f43..02529557 100644
--- a/tests/testthat/test-utils-extract.R
+++ b/tests/testthat/test-utils-extract.R
@@ -19,6 +19,9 @@ test_that("qmd_to_r_script() errors on existing script", {
 
 test_that("qmd_to_r_script() writes R file that renders", {
   skip_if_no_quarto()
+  # TODO: Problem with quarto 1.9 - reactivate when fix.
+  # https://github.com/quarto-dev/quarto-cli/issues/14529
+  skip_if_quarto("1.9")
   r_script <- withr::local_tempfile(pattern = "purl", fileext = ".R")
 
   announce_snapshot_file(name = "purl.R")