diff --git a/NAMESPACE b/NAMESPACE
index e7571aeea..af48705aa 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -67,7 +67,6 @@ export(tutorial_html_dependency)
 export(tutorial_options)
 export(tutorial_package_dependencies)
 import(curl)
-import(rmarkdown)
 import(shiny)
 importFrom(evaluate,evaluate)
 importFrom(htmltools,HTML)
diff --git a/NEWS.md b/NEWS.md
index 697ac3b40..5ecfcfbe5 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -57,6 +57,7 @@ learnr (development version)
 
 ## Bug fixes
 
+* learnr's knitr hooks are now included by default in the `learnr::tutorial` R Markdown format. They are also registered for any tutorials run by `run_tutorial()`. [thanks @czucca, #599](https://github.com/rstudio/learnr/pull/599)
 * Support the updated Bootstrap 4+ popover `dispose` method name, previously `destroy`. ([#560](https://github.com/rstudio/learnr/pull/560))
 * Properly enforce time limits and measure exercise execution times that exceed 60 seconds ([#366](https://github.com/rstudio/learnr/pull/366), [#368](https://github.com/rstudio/learnr/pull/368))
 * Fixed unexpected behavior for `question_is_correct.learnr_text()` where `trim = FALSE`. Comparisons will now happen with the original input value, not the `HTML()` formatted answer value. ([#376](https://github.com/rstudio/learnr/pull/376))
diff --git a/R/knitr-hooks.R b/R/knitr-hooks.R
index f8101131f..d8b59c072 100644
--- a/R/knitr-hooks.R
+++ b/R/knitr-hooks.R
@@ -13,12 +13,7 @@ detect_installed_knitr_hooks <- function() {
   is.function(tutorial_knit_hook)
 }
 
-install_knitr_hooks <- function() {
-  # set global tutorial option which we can use as a basis for hooks
-  # (this is so we don't collide with hooks set by the user or
-  # by other packages or Rmd output formats)
-  knitr::opts_chunk$set(tutorial = TRUE)
-
+tutorial_knitr_options <- function() {
   # helper to check for runtime: shiny_prerendered being active
   is_shiny_prerendered_active <- function() {
     identical(knitr::opts_knit$get("rmarkdown.runtime"),"shiny_prerendered")
@@ -186,7 +181,7 @@ install_knitr_hooks <- function() {
   }
 
   # hook to turn off evaluation/highlighting for exercise related chunks
-  knitr::opts_hooks$set(tutorial = function(options) {
+  tutorial_opts_hook <-  function(options) {
 
     # check for chunk type
     exercise_chunk <- is_exercise_chunk(options)
@@ -285,10 +280,10 @@ install_knitr_hooks <- function() {
 
     # return modified options
     options
-  })
+  }
 
   # hook to amend output for exercise related chunks
-  knitr::knit_hooks$set(tutorial = function(before, options, envir) {
+  tutorial_knit_hook <- function(before, options, envir) {
 
     # helper to produce an exercise wrapper div w/ the specified class
     exercise_wrapper_div <- function(suffix = NULL, extra_html = NULL) {
@@ -465,7 +460,24 @@ install_knitr_hooks <- function() {
       }
 
     }
-  })
+  }
+
+  list(
+    # learnr uses `tutorial` for options and hooks, and we also globally set the
+    # chunk option `tutorial = TRUE`. This allows the learnr tutorial hooks to
+    # visit every chunk without colliding with hooks or options set by other
+    # packages or Rmd formats.
+    opts_chunk = list(tutorial = TRUE),
+    opts_hooks = list(tutorial = tutorial_opts_hook),
+    knit_hooks = list(tutorial = tutorial_knit_hook)
+  )
+}
+
+install_knitr_hooks <- function() {
+  knit_opts <- tutorial_knitr_options()
+  knitr::opts_chunk$set(tutorial = knit_opts$opts_chunk$tutorial)
+  knitr::opts_hooks$set(tutorial = knit_opts$opts_hooks$tutorial)
+  knitr::knit_hooks$set(tutorial = knit_opts$knit_hooks$tutorial)
 }
 
 remove_knitr_hooks <- function() {
diff --git a/R/learnr-package.R b/R/learnr-package.R
new file mode 100644
index 000000000..648184db2
--- /dev/null
+++ b/R/learnr-package.R
@@ -0,0 +1,34 @@
+#' @keywords internal
+"_PACKAGE"
+
+## usethis namespace: start
+#' @importFrom evaluate evaluate
+#' @importFrom htmltools attachDependencies
+#' @importFrom htmltools div
+#' @importFrom htmltools HTML
+#' @importFrom htmltools htmlDependency
+#' @importFrom htmltools tags
+#' @importFrom htmlwidgets createWidget
+#' @importFrom jsonlite base64_dec
+#' @importFrom jsonlite base64_enc
+#' @importFrom knitr all_labels
+#' @importFrom knitr knit_hooks
+#' @importFrom knitr knit_meta_add
+#' @importFrom knitr opts_chunk
+#' @importFrom knitr opts_hooks
+#' @importFrom knitr opts_knit
+#' @importFrom knitr spin
+#' @importFrom markdown markdownExtensions
+#' @importFrom markdown markdownToHTML
+#' @importFrom rprojroot find_root
+#' @importFrom rprojroot is_r_package
+#' @importFrom shiny invalidateLater
+#' @importFrom shiny isolate
+#' @importFrom shiny observe
+#' @importFrom shiny observeEvent
+#' @importFrom shiny reactive
+#' @importFrom shiny reactiveValues
+#' @importFrom shiny req
+#' @importFrom withr with_envvar
+## usethis namespace: end
+NULL
diff --git a/R/package.R b/R/package.R
deleted file mode 100644
index a0320e6b6..000000000
--- a/R/package.R
+++ /dev/null
@@ -1,23 +0,0 @@
-
-#' @import rmarkdown
-#' @importFrom htmltools htmlDependency attachDependencies HTML div tags
-#' @importFrom knitr opts_chunk opts_knit opts_hooks knit_hooks knit_meta_add all_labels spin
-#' @importFrom jsonlite base64_dec base64_enc
-#' @importFrom htmlwidgets createWidget
-#' @importFrom markdown markdownToHTML markdownExtensions
-#' @importFrom evaluate evaluate
-#' @importFrom withr with_envvar
-#' @importFrom rprojroot find_root is_r_package
-#' @importFrom shiny reactiveValues observeEvent req isolate invalidateLater isolate observe reactive
-NULL
-
-# install knitr hooks when package is attached to search path
-.onAttach <- function(libname, pkgname) {
-  install_knitr_hooks()
-  initialize_tutorial()
-}
-
-# remove knitr hooks when package is detached from search path
-.onDetach <- function(libpath) {
-  remove_knitr_hooks()
-}
diff --git a/R/run.R b/R/run.R
index e8c7f2723..4a5ecc3f5 100644
--- a/R/run.R
+++ b/R/run.R
@@ -84,6 +84,12 @@ run_tutorial <- function(name = NULL, package = NULL, shiny_args = NULL) {
       )
     })
 
+  # ensure hooks are available for a tutorial and clean up after run_tutorial()
+  if (!detect_installed_knitr_hooks()) {
+    withr::defer(remove_knitr_hooks())
+  }
+  install_knitr_hooks()
+
   # run within tutorial wd
   withr::with_dir(tutorial_path, {
     if (!identical(Sys.getenv("SHINY_PORT", ""), "")) {
diff --git a/R/tutorial-format.R b/R/tutorial-format.R
index f0df3c96e..4260bb5b9 100644
--- a/R/tutorial-format.R
+++ b/R/tutorial-format.R
@@ -62,13 +62,13 @@ tutorial <- function(fig_width = 6.5,
   args <- c(args, "--section-divs")
 
   # template
-  args <- c(args, "--template", pandoc_path_arg(
+  args <- c(args, "--template", rmarkdown::pandoc_path_arg(
     system.file("rmarkdown/templates/tutorial/resources/tutorial-format.htm",
                 package = "learnr")
   ))
 
   # content includes
-  args <- c(args, includes_to_pandoc_args(includes))
+  args <- c(args, rmarkdown::includes_to_pandoc_args(includes))
 
   # pagedtables
   if (identical(df_print, "paged")) {
@@ -94,7 +94,7 @@ tutorial <- function(fig_width = 6.5,
 
   # additional css
   for (css_file in css)
-    args <- c(args, "--css", pandoc_path_arg(css_file))
+    args <- c(args, "--css", rmarkdown::pandoc_path_arg(css_file))
 
   # resolve theme (ammend base stylesheet for "rstudio" theme
   stylesheets <- "tutorial-format.css"
@@ -123,16 +123,19 @@ tutorial <- function(fig_width = 6.5,
 
   # additional pandoc variables
   jsbool <- function(value) ifelse(value, "true", "false")
-  args <- c(args, pandoc_variable_arg("progressive", jsbool(progressive)))
-  args <- c(args, pandoc_variable_arg("allow-skip", jsbool(allow_skip)))
+  args <- c(args, rmarkdown::pandoc_variable_arg("progressive", jsbool(progressive)))
+  args <- c(args, rmarkdown::pandoc_variable_arg("allow-skip", jsbool(allow_skip)))
 
   # knitr and pandoc options
-  knitr_options <- knitr_options_html(fig_width, fig_height, fig_retina, keep_md = FALSE , dev)
-  pandoc_options <- pandoc_options(to = "html4",
+  knitr_options <- rmarkdown::knitr_options_html(fig_width, fig_height, fig_retina, keep_md = FALSE , dev)
+  pandoc_options <- rmarkdown::pandoc_options(to = "html4",
     from = rmarkdown::from_rmarkdown(fig_caption, md_extensions),
     args = args,
     ext = ".html")
 
+  tutorial_opts <- tutorial_knitr_options()
+  knitr_options <- utils::modifyList(knitr_options, tutorial_opts)
+
   # set 1000 as the default maximum number of rows in paged tables
   knitr_options$opts_chunk$max.print <- 1000
 
diff --git a/R/learnr.R b/R/zzz.R
similarity index 68%
rename from R/learnr.R
rename to R/zzz.R
index c65bd5b09..19e324658 100644
--- a/R/learnr.R
+++ b/R/zzz.R
@@ -1,3 +1,15 @@
+
+# install knitr hooks when package is attached to search path
+.onAttach <- function(libname, pkgname) {
+  install_knitr_hooks()
+  initialize_tutorial()
+}
+
+# remove knitr hooks when package is detached from search path
+.onDetach <- function(libpath) {
+  remove_knitr_hooks()
+}
+
 .onLoad <- function(libname, pkgname) {
   register_default_event_handlers()
 
diff --git a/man/learnr-package.Rd b/man/learnr-package.Rd
new file mode 100644
index 000000000..dc21654ab
--- /dev/null
+++ b/man/learnr-package.Rd
@@ -0,0 +1,42 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/learnr-package.R
+\docType{package}
+\name{learnr-package}
+\alias{learnr}
+\alias{learnr-package}
+\title{learnr: Interactive Tutorials for R}
+\description{
+Create interactive tutorials using R Markdown. Use a combination of narrative, figures, videos, exercises, and quizzes to create self-paced tutorials for learning about R and R packages.
+}
+\seealso{
+Useful links:
+\itemize{
+  \item \url{https://rstudio.github.io/learnr/}
+  \item \url{https://github.com/rstudio/learnr}
+  \item Report bugs at \url{https://github.com/rstudio/learnr/issues}
+}
+
+}
+\author{
+\strong{Maintainer}: Garrick Aden-Buie \email{garrick@rstudio.com} (\href{https://orcid.org/0000-0002-7111-0077}{ORCID})
+
+Authors:
+\itemize{
+  \item Barret Schloerke \email{barret@rstudio.com} (\href{https://orcid.org/0000-0001-9986-114X}{ORCID})
+  \item JJ Allaire \email{jj@rstudio.com} [conceptor]
+}
+
+Other contributors:
+\itemize{
+  \item Alexander Rossell Hayes \email{alex.rossellhayes@rstudio.com} (\href{https://orcid.org/0000-0001-9412-0457}{ORCID}) [contributor]
+  \item Nischal Shrestha \email{nischal@rstudio.com} (\href{https://orcid.org/0000-0003-3321-1712}{ORCID}) [contributor]
+  \item Angela Li \email{angelali921@gmail.com} (vignette) [contributor]
+  \item RStudio [copyright holder, funder]
+  \item  Ajax.org B.V. (Ace library) [contributor, copyright holder]
+  \item Zeno Rocha (clipboard.js library) [contributor, copyright holder]
+  \item Nick Payne (Bootbox library) [contributor, copyright holder]
+  \item Jake Archibald (idb-keyval library) [contributor, copyright holder]
+}
+
+}
+\keyword{internal}