diff --git a/R/build-article.R b/R/build-article.R
index d7fc69cdc..84ec3dafd 100644
--- a/R/build-article.R
+++ b/R/build-article.R
@@ -13,8 +13,9 @@ build_article <- function(name,
                           seed = 1014L,
                           new_process = TRUE,
                           pandoc_args = character(),
+                          override = list(),
                           quiet = TRUE) {
-  pkg <- as_pkgdown(pkg)
+  pkg <- section_init(pkg, "articles", override = override)
 
   # Look up in pkg vignette data - this allows convenient automatic
   # specification of depth, output destination, and other parameters that
diff --git a/R/build-articles.R b/R/build-articles.R
index b3a626b0f..6f095bb63 100644
--- a/R/build-articles.R
+++ b/R/build-articles.R
@@ -199,7 +199,7 @@ build_articles <- function(pkg = ".",
                            seed = 1014L,
                            override = list(),
                            preview = FALSE) {
-  pkg <- section_init(pkg, depth = 1L, override = override)
+  pkg <- section_init(pkg, "articles", override = override)
   check_bool(quiet)
   check_bool(lazy)
   check_number_whole(seed, allow_null = TRUE)
@@ -228,10 +228,8 @@ build_articles <- function(pkg = ".",
 #' @export
 #' @rdname build_articles
 #' @order 3
-build_articles_index <- function(pkg = ".") {
-  pkg <- as_pkgdown(pkg)
-
-  create_subdir(pkg, "articles")
+build_articles_index <- function(pkg = ".", override = list()) {
+  pkg <- section_init(pkg, "articles", override = override)
   render_page(
     pkg,
     "article-index",
diff --git a/R/build-home-index.R b/R/build-home-index.R
index 36801a8c9..cf5cf79d9 100644
--- a/R/build-home-index.R
+++ b/R/build-home-index.R
@@ -1,7 +1,7 @@
 #' @export
 #' @rdname build_home
-build_home_index <- function(pkg = ".", quiet = TRUE) {
-  pkg <- section_init(pkg, depth = 0L)
+build_home_index <- function(pkg = ".", override = list(), quiet = TRUE) {
+  pkg <- section_init(pkg, override = override)
 
   src_path <- path_index(pkg)
   dst_path <- path(pkg$dst_path, "index.html")
diff --git a/R/build-home.R b/R/build-home.R
index 194ca69a8..ec06a6e64 100644
--- a/R/build-home.R
+++ b/R/build-home.R
@@ -291,11 +291,10 @@ build_home <- function(pkg = ".",
                        preview = FALSE,
                        quiet = TRUE) {
 
-  pkg <- section_init(pkg, depth = 0L, override = override)
+  pkg <- section_init(pkg, override = override)
   check_bool(quiet)
 
   cli::cli_rule("Building home")
-  create_subdir(pkg, "")
 
   build_citation_authors(pkg)
 
diff --git a/R/build-news.R b/R/build-news.R
index 9ebc1e6ef..da554025a 100644
--- a/R/build-news.R
+++ b/R/build-news.R
@@ -75,12 +75,11 @@
 build_news <- function(pkg = ".",
                        override = list(),
                        preview = FALSE) {
-  pkg <- section_init(pkg, depth = 1L, override = override)
+  pkg <- section_init(pkg, "news", override = override)
   if (!has_news(pkg$src_path))
     return(invisible())
 
   cli::cli_rule("Building news")
-  create_subdir(pkg, "news")
 
   one_page <- config_pluck_bool(pkg, "news.one_page", default = TRUE)
   if (one_page) {
diff --git a/R/build-redirects.R b/R/build-redirects.R
index f4e4fc735..ac55a0f04 100644
--- a/R/build-redirects.R
+++ b/R/build-redirects.R
@@ -25,7 +25,7 @@
 #' @export
 build_redirects <- function(pkg = ".",
                             override = list()) {
-  pkg <- section_init(pkg, depth = 1L, override = override)
+  pkg <- section_init(pkg, override = override)
   has_url <- !is.null(config_pluck_string(pkg, "url"))
 
   redirects <- data_redirects(pkg, has_url)
diff --git a/R/build-reference.R b/R/build-reference.R
index 70550d540..de8992149 100644
--- a/R/build-reference.R
+++ b/R/build-reference.R
@@ -158,7 +158,7 @@ build_reference <- function(pkg = ".",
                             preview = FALSE,
                             devel = TRUE,
                             topics = NULL) {
-  pkg <- section_init(pkg, depth = 1L, override = override)
+  pkg <- section_init(pkg, "reference", override = override)
   check_bool(lazy)
   check_bool(examples)
   check_bool(run_dont_run)
@@ -242,9 +242,8 @@ examples_env <- function(pkg, seed = 1014L, devel = TRUE, envir = parent.frame()
 
 #' @export
 #' @rdname build_reference
-build_reference_index <- function(pkg = ".") {
-  pkg <- section_init(pkg, depth = 1L)
-  create_subdir(pkg, "reference")
+build_reference_index <- function(pkg = ".", override = list()) {
+  pkg <- section_init(pkg, "reference", override = override)
 
   # Copy icons, if needed
   dir_copy_to(
diff --git a/R/build-search-docs.R b/R/build-search-docs.R
index f1a2fad18..788d00525 100644
--- a/R/build-search-docs.R
+++ b/R/build-search-docs.R
@@ -79,8 +79,9 @@ build_sitemap <- function(pkg = ".") {
 #'
 build_search <- function(pkg = ".",
                          override = list()) {
-  pkg <- section_init(pkg, depth = 1L, override = override)
+  pkg <- section_init(pkg, override = override)
   cli::cli_rule("Building search index")
+
   search_index <- build_search_index(pkg)
   jsonlite::write_json(
     search_index,
diff --git a/R/build-tutorials.R b/R/build-tutorials.R
index 6157f4e30..006f9f72f 100644
--- a/R/build-tutorials.R
+++ b/R/build-tutorials.R
@@ -29,7 +29,7 @@
 #' @family site components
 #' @export
 build_tutorials <- function(pkg = ".", override = list(), preview = FALSE) {
-  pkg <- section_init(pkg, depth = 1L, override = override)
+  pkg <- section_init(pkg, "tutorials", override = override)
 
   tutorials <- pkg$tutorials
 
@@ -38,7 +38,6 @@ build_tutorials <- function(pkg = ".", override = list(), preview = FALSE) {
   }
 
   cli::cli_rule("Building tutorials")
-  create_subdir(pkg, "tutorials")
 
   data <- purrr::transpose(tutorials)
 
diff --git a/R/build.R b/R/build.R
index 7434d61ae..1889c4a9b 100644
--- a/R/build.R
+++ b/R/build.R
@@ -422,7 +422,7 @@ build_site_local <- function(pkg = ".",
                              preview = NA,
                              devel = TRUE) {
 
-  pkg <- section_init(pkg, depth = 0, override = override)
+  pkg <- section_init(pkg, override = override)
 
   cli::cli_rule("Building pkgdown site for package {.pkg {pkg$package}}")
   cli::cli_inform("Reading from: {src_path(path_abs(pkg$src_path))}")
diff --git a/R/clean.R b/R/clean.R
index 6116f3ae8..6c4ba235d 100644
--- a/R/clean.R
+++ b/R/clean.R
@@ -15,8 +15,8 @@ clean_site <- function(pkg = ".", quiet = FALSE) {
 
   if (!dir_exists(pkg$dst_path)) return(invisible())
 
-  top_level <- dir_ls(pkg$dst_path)
-  top_level <- top_level[!path_file(top_level) %in% c("CNAME", "dev")]
+  check_dest_is_pkgdown(pkg)
+  top_level <- dest_files(pkg)
 
   is_dir <- is_dir(top_level)
   dir_delete(top_level[is_dir])
@@ -24,3 +24,25 @@ clean_site <- function(pkg = ".", quiet = FALSE) {
 
   invisible(TRUE)
 }
+
+check_dest_is_pkgdown <- function(pkg) {
+  if (file_exists(path(pkg$dst_path, "pkgdown.yml"))) {
+    return()
+  }
+
+  cli::cli_abort(c(
+    "{.file {pkg$dst_path}} is non-empty and not built by pkgdown",
+    "!" = "Make sure it contains no important information \\
+            and use {.run pkgdown::clean_site()} to delete its contents."
+    )
+  )
+}
+
+dest_files <- function(pkg) {
+  if (!dir_exists(pkg$dst_path)) {
+    character()
+  } else {
+    top_level <- dir_ls(pkg$dst_path)
+    top_level[!path_file(top_level) %in% c("CNAME", "dev")]  
+  }
+}
diff --git a/R/context.R b/R/context.R
index a82ecc0b6..a0fd58e45 100644
--- a/R/context.R
+++ b/R/context.R
@@ -1,7 +1,23 @@
-section_init <- function(pkg, depth, override = list(), .frame = parent.frame()) {
+section_init <- function(pkg,
+                         subdir = NULL,
+                         override = list(),
+                         .frame = parent.frame()) {
+  rstudio_save_all()
   pkg <- as_pkgdown(pkg, override = override)
+  
+  if (length(dest_files(pkg)) > 0) {
+    check_dest_is_pkgdown(pkg) 
+  } else {
+    init_site(pkg)
+  }
+ 
+  if (is.null(subdir)) {
+    depth <- 0
+  } else {
+    depth <- 1
+    dir_create(path(pkg$dst_path, subdir))
+  }
 
-  rstudio_save_all()
   local_envvar_pkgdown(pkg, .frame)
   local_options_link(pkg, depth = depth, .frame = .frame)
 
diff --git a/R/init.R b/R/init.R
index 90ddc21d3..25516ec32 100644
--- a/R/init.R
+++ b/R/init.R
@@ -20,17 +20,11 @@
 #'
 #' @inheritParams build_articles
 #' @export
-init_site <- function(pkg = ".") {
-  pkg <- as_pkgdown(pkg)
-
-  if (is_non_pkgdown_site(pkg$dst_path)) {
-    cli::cli_abort(c(
-      "{.file {pkg$dst_path}} is non-empty and not built by pkgdown",
-      "!" = "Make sure it contains no important information \\
-             and use {.run pkgdown::clean_site()} to delete its contents."
-      )
-    )
-  }
+init_site <- function(pkg = ".", override = list()) {
+  # This is the only user facing function that doesn't call section_init()
+  # because section_init() can conditionally call init_site()
+  rstudio_save_all()
+  pkg <- as_pkgdown(pkg, override = override)
 
   cli::cli_rule("Initialising site")
   dir_create(pkg$dst_path)
@@ -156,14 +150,3 @@ site_meta <- function(pkg) {
 
   print_yaml(yaml)
 }
-
-is_non_pkgdown_site <- function(dst_path) {
-  if (!dir_exists(dst_path)) {
-    return(FALSE)
-  }
-
-  top_level <- dir_ls(dst_path)
-  top_level <- top_level[!path_file(top_level) %in% c("CNAME", "dev", "deps")]
-
-  length(top_level) >= 1 && !"pkgdown.yml" %in% path_file(top_level)
-}
diff --git a/R/pkgdown.R b/R/pkgdown.R
index 3ecf33449..ef88c1100 100644
--- a/R/pkgdown.R
+++ b/R/pkgdown.R
@@ -25,6 +25,11 @@ local_pkgdown_site <- function(path = NULL,
   check_string(path, allow_null = TRUE)
 
   dst_path <- withr::local_tempdir(.local_envir = env)
+  # Simulate init_site() so we only have to run it if we care about <head>
+  file_create(path(dst_path, "pkgdown.yml"))
+  dir_create(path(dst_path, "deps"))
+  file_create(path(dst_path, "deps", "data-deps.txt"))
+
   meta <- modify_list(meta, list(destination = dst_path))
 
   if (is.null(path)) {
@@ -46,12 +51,8 @@ local_pkgdown_site <- function(path = NULL,
     # Make it a bit easier to create other files
     dir_create(path(path, "R"))
     dir_create(path(path, "vignettes"))
-
-    # Create dummy deps so it's not 100% necessary to run init_site()
-    dir_create(path(dst_path, "deps"))
-    file_create(path(dst_path, "deps", "data-deps.txt"))
   }
-
+  
   as_pkgdown(path, meta)
 }
 
diff --git a/R/utils-fs.R b/R/utils-fs.R
index f424d1e09..5c1b98b02 100644
--- a/R/utils-fs.R
+++ b/R/utils-fs.R
@@ -52,15 +52,6 @@ file_copy_to <- function(src_paths,
   file_copy(src_paths[!eq], dst_paths[!eq], overwrite = TRUE)
 }
 
-# Checks init_site() first.
-create_subdir <- function(pkg, subdir) {
-  if (!dir_exists(pkg$dst_path)) {
-    init_site(pkg)
-  }
-  dir_create(path(pkg$dst_path, subdir))
-
-}
-
 out_of_date <- function(source, target, call = caller_env()) {
   if (!file_exists(target)) {
     return(TRUE)
diff --git a/man/build_articles.Rd b/man/build_articles.Rd
index e6f89ecee..f5be82a18 100644
--- a/man/build_articles.Rd
+++ b/man/build_articles.Rd
@@ -22,10 +22,11 @@ build_article(
   seed = 1014L,
   new_process = TRUE,
   pandoc_args = character(),
+  override = list(),
   quiet = TRUE
 )
 
-build_articles_index(pkg = ".")
+build_articles_index(pkg = ".", override = list())
 }
 \arguments{
 \item{pkg}{Path to package.}
diff --git a/man/build_home.Rd b/man/build_home.Rd
index b854a52e3..9db92d68c 100644
--- a/man/build_home.Rd
+++ b/man/build_home.Rd
@@ -7,7 +7,7 @@
 \usage{
 build_home(pkg = ".", override = list(), preview = FALSE, quiet = TRUE)
 
-build_home_index(pkg = ".", quiet = TRUE)
+build_home_index(pkg = ".", override = list(), quiet = TRUE)
 }
 \arguments{
 \item{pkg}{Path to package.}
diff --git a/man/build_reference.Rd b/man/build_reference.Rd
index 4d1388429..3ae9edd16 100644
--- a/man/build_reference.Rd
+++ b/man/build_reference.Rd
@@ -17,7 +17,7 @@ build_reference(
   topics = NULL
 )
 
-build_reference_index(pkg = ".")
+build_reference_index(pkg = ".", override = list())
 }
 \arguments{
 \item{pkg}{Path to package.}
diff --git a/man/init_site.Rd b/man/init_site.Rd
index 5e0638c91..9d44cc1aa 100644
--- a/man/init_site.Rd
+++ b/man/init_site.Rd
@@ -4,10 +4,13 @@
 \alias{init_site}
 \title{Initialise site infrastructure}
 \usage{
-init_site(pkg = ".")
+init_site(pkg = ".", override = list())
 }
 \arguments{
 \item{pkg}{Path to package.}
+
+\item{override}{An optional named list used to temporarily override
+values in \verb{_pkgdown.yml}}
 }
 \description{
 \code{init_site()}: