diff --git a/NEWS.md b/NEWS.md
index ae9bf37af..f512993bd 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,5 +1,8 @@
 # renv (development version)
 
+* Fixed an issue that could cause code within a project `.Rprofile` to execute
+  before the project had been loaded in RStudio. (#1650)
+
 * `renv::snapshot()` and `renv::status()` gain the `dev` argument. This
   can be used when you'd like to capture package dependencies from
   the *Suggests* field of your package's DESCRIPTION file. (#1019)
diff --git a/R/bootstrap.R b/R/bootstrap.R
index a314eecef..61a0bca5f 100644
--- a/R/bootstrap.R
+++ b/R/bootstrap.R
@@ -957,16 +957,3 @@ renv_bootstrap_run <- function(version, libpath) {
   warning(paste(msg, collapse = "\n"), call. = FALSE)
 
 }
-
-
-renv_bootstrap_in_rstudio <- function() {
-  commandArgs()[[1]] == "RStudio"
-}
-
-# Used to work around buglet in RStudio if hook uses readline
-renv_bootstrap_flush_console <- function() {
-  tryCatch({
-    tools <- as.environment("tools:rstudio")
-    tools$.rs.api.sendToConsole("", echo = FALSE, focus = FALSE)
-  }, error = function(cnd) {})
-}
diff --git a/R/load.R b/R/load.R
index dd0ef7b45..9325ebb4a 100644
--- a/R/load.R
+++ b/R/load.R
@@ -139,12 +139,23 @@ renv_load_action <- function(project) {
   if (!interactive())
     return("load")
 
-  # if this project doesn't yet contain an 'renv' folder, assume
-  # that it has not yet been initialized, and prompt the user
+  # if this project already contains an 'renv' folder, assume it's
+  # already been initialized and we can directly load it
   renv <- renv_paths_renv(project = project, profile = FALSE)
   if (dir.exists(renv))
     return("load")
 
+  # if we're running within RStudio at this point, and we're running
+  # within the auto-loader, we need to defer execution here so that
+  # the console is able to properly receive user input and update
+  # https://github.com/rstudio/renv/issues/1650
+  autoloading <- getOption("renv.autoloader.running", default = FALSE)
+  if (autoloading && renv_rstudio_available()) {
+    setHook("rstudio.sessionInit", function() {
+      renv::load(project)
+    })
+  }
+
   # check and see if we're being called within a sub-directory
   path <- renv_file_find(dirname(project), function(parent) {
     if (file.exists(file.path(parent, "renv")))
diff --git a/inst/resources/activate.R b/inst/resources/activate.R
index aad8bc2bb..857bd0dc9 100644
--- a/inst/resources/activate.R
+++ b/inst/resources/activate.R
@@ -1034,19 +1034,6 @@ local({
   
   }
   
-  
-  renv_bootstrap_in_rstudio <- function() {
-    commandArgs()[[1]] == "RStudio"
-  }
-  
-  # Used to work around buglet in RStudio if hook uses readline
-  renv_bootstrap_flush_console <- function() {
-    tryCatch({
-      tools <- as.environment("tools:rstudio")
-      tools$.rs.api.sendToConsole("", echo = FALSE, focus = FALSE)
-    }, error = function(cnd) {})
-  }
-  
   renv_json_read <- function(file = NULL, text = NULL) {
   
     jlerr <- NULL
@@ -1185,16 +1172,8 @@ local({
   # construct full libpath
   libpath <- file.path(root, prefix)
 
-  if (renv_bootstrap_in_rstudio()) {
-    # RStudio only updates console once .Rprofile is finished, so
-    # instead run code on sessionInit
-    setHook("rstudio.sessionInit", function(...) {
-      renv_bootstrap_exec(project, libpath, version)
-      renv_bootstrap_flush_console()
-    })
-  } else {
-    renv_bootstrap_exec(project, libpath, version)
-  }
+  # run bootstrap code
+  renv_bootstrap_exec(project, libpath, version)
 
   invisible()
 
diff --git a/templates/template-activate.R b/templates/template-activate.R
index 05fb9f145..8d0801d26 100644
--- a/templates/template-activate.R
+++ b/templates/template-activate.R
@@ -88,16 +88,8 @@ local({
   # construct full libpath
   libpath <- file.path(root, prefix)
 
-  if (renv_bootstrap_in_rstudio()) {
-    # RStudio only updates console once .Rprofile is finished, so
-    # instead run code on sessionInit
-    setHook("rstudio.sessionInit", function(...) {
-      renv_bootstrap_exec(project, libpath, version)
-      renv_bootstrap_flush_console()
-    })
-  } else {
-    renv_bootstrap_exec(project, libpath, version)
-  }
+  # run bootstrap code
+  renv_bootstrap_exec(project, libpath, version)
 
   invisible()