diff --git a/.github/workflows/bootstrap_script.yml b/.github/workflows/bootstrap_script.yml
index e46f5cb41e..c0ade9843b 100644
--- a/.github/workflows/bootstrap_script.yml
+++ b/.github/workflows/bootstrap_script.yml
@@ -107,12 +107,14 @@ jobs:
           EB_BOOTSTRAP_VERSION=$(grep '^EB_BOOTSTRAP_VERSION' easybuild/scripts/bootstrap_eb.py | sed 's/[^0-9.]//g')
           EB_BOOTSTRAP_SHA256SUM=$(sha256sum easybuild/scripts/bootstrap_eb.py | cut -f1 -d' ')
           EB_BOOTSTRAP_FOUND="$EB_BOOTSTRAP_VERSION $EB_BOOTSTRAP_SHA256SUM"
-          EB_BOOTSTRAP_EXPECTED="20210106.01 c2d93de0dd91123eb4f51cfc16d1f5efb80f1d238b3d6cd100994086887a1ae0"
+          EB_BOOTSTRAP_EXPECTED="20210618.01 e5d477d717c6d3648ba2027ab735713ba5804fbf52f4b4adcca0bc1379b44618"
           test "$EB_BOOTSTRAP_FOUND" = "$EB_BOOTSTRAP_EXPECTED" || (echo "Version check on bootstrap script failed $EB_BOOTSTRAP_FOUND" && exit 1)
 
           # test bootstrap script
           export PREFIX=/tmp/$USER/$GITHUB_SHA/eb_bootstrap
+          export EASYBUILD_BOOTSTRAP_DEPRECATED=1
           python easybuild/scripts/bootstrap_eb.py $PREFIX
+          unset EASYBUILD_BOOTSTRAP_DEPRECATED
           # unset $PYTHONPATH to avoid mixing two EasyBuild 'installations' when testing bootstrapped EasyBuild module
           unset PYTHONPATH
           # simple sanity check on bootstrapped EasyBuild module
diff --git a/easybuild/scripts/bootstrap_eb.py b/easybuild/scripts/bootstrap_eb.py
index 1ccc317466..ed3390ea93 100644
--- a/easybuild/scripts/bootstrap_eb.py
+++ b/easybuild/scripts/bootstrap_eb.py
@@ -62,7 +62,7 @@
     import urllib.request as std_urllib
 
 
-EB_BOOTSTRAP_VERSION = '20210106.01'
+EB_BOOTSTRAP_VERSION = '20210618.01'
 
 # argparse preferrred, optparse deprecated >=2.7
 HAVE_ARGPARSE = False
@@ -82,6 +82,9 @@
 
 STAGE1_SUBDIR = 'eb_stage1'
 
+# the EasyBuild bootstrap script is deprecated, and will only run if $EASYBUILD_BOOTSTRAP_DEPRECATED is defined
+EASYBUILD_BOOTSTRAP_DEPRECATED = os.environ.pop('EASYBUILD_BOOTSTRAP_DEPRECATED', None)
+
 # set print_debug to True for detailed progress info
 print_debug = os.environ.pop('EASYBUILD_BOOTSTRAP_DEBUG', False)
 
@@ -854,6 +857,17 @@ def main():
     self_txt = open(__file__).read()
     if IS_PY3:
         self_txt = self_txt.encode('utf-8')
+
+    url = 'https://docs.easybuild.io/en/latest/Installation.html'
+    info("Use of the EasyBuild boostrap script is DEPRECATED (since June 2021).")
+    info("It is strongly recommended to use one of the installation methods outlined at %s instead!\n" % url)
+    if not EASYBUILD_BOOTSTRAP_DEPRECATED:
+        error("The EasyBuild bootstrap script will only run if $EASYBUILD_BOOTSTRAP_DEPRECATED is defined.")
+    else:
+        msg = "You have opted to continue with the EasyBuild bootstrap script by defining "
+        msg += "$EASYBUILD_BOOTSTRAP_DEPRECATED. Good luck!\n"
+        info(msg)
+
     info("EasyBuild bootstrap script (version %s, MD5: %s)" % (EB_BOOTSTRAP_VERSION, md5(self_txt).hexdigest()))
     info("Found Python %s\n" % '; '.join(sys.version.split('\n')))