diff --git a/README.md b/README.md
index e99bc2c..7e0344f 100644
--- a/README.md
+++ b/README.md
@@ -98,8 +98,8 @@ of GNU/Linux distributions. The needed executables in the host OS are:
 - bash
 - wget or curl
 - tar
-- id
 - mkdir
+- chown (for root access only)
 
 The minimum recommended linux kernel is 2.6.0+
 
@@ -171,24 +171,20 @@ To quick fix this, you can just install a fonts package:
     pacman -S gnu-free-fonts
 ```
 
-###Missing permissions on removing a package###
-- **Q**: Why I cannot remove the package I have installed?
+###Differences between filesystem and package ownership###
+- **Q**: Why do I get warning when I install a package using root privileges?
 ```
-    pacman -Rsn lsof
-    checking dependencies...
-
-    Packages (1): lsof-4.88-1
-
-    Total Removed Size:   0.21 MiB
-
-    error: cannot remove /usr/share/licenses/lsof/LICENSE (Permission denied)
-    error: could not remove database entry lsof-4.88-1
+    pacman -S systat
+    ...
+    warning: directory ownership differs on /usr/
+    filesystem: 1000:100  package: 0:0
+    ...
 ```
 
-- **A**: This is probably because you have installed the package with root
-permissions. Since JuJu gives the possibility to install packages
-either as root or as normal user you need to remember that and remove
-the package with the right user!
+- **A**: In these cases the package installation went smoothly anyway.
+This should happen every time you install package with root privileges
+since JuJu will try to preserve the JuJu environment by assigning ownership
+of the files to the real user.
 
 ###No servers configured for repository###
 -**Q**: Why I cannot install packages?
diff --git a/lib/core.sh b/lib/core.sh
index d5d9a27..de17eaf 100644
--- a/lib/core.sh
+++ b/lib/core.sh
@@ -73,8 +73,9 @@ PROOT_LINK=http://static.proot.me/proot-${ARCH}
 
 SH=("/bin/sh" "--login")
 CHROOT=${JUJU_HOME}/usr/bin/arch-chroot
-TRUE=${JUJU_HOME}/usr/bin/true
-ID="${JUJU_HOME}/usr/bin/id -u"
+TRUE=/usr/bin/true
+ID="/usr/bin/id -u"
+CHOWN="/usr/bin/chown"
 
 ################################# MAIN FUNCTIONS ##############################
 
@@ -148,16 +149,23 @@ function setup_from_file_juju(){
 }
 
 
-function _define_chroot_args(){
-    local comm=${SH[@]}
-    [ "$1" != "" ] && comm="$@"
-    echo $comm
-}
-
-
 function run_juju_as_root(){
-    mkdir -p ${JUJU_HOME}/${HOME}
-    JUJU_ENV=1 ${CHROOT} $JUJU_HOME /usr/bin/bash -c "mkdir -p /run/lock && $(_define_chroot_args "$@")"
+    local main_cmd="${SH[@]}"
+    [ "$1" != "" ] && main_cmd="$@"
+
+    local uid=$UID
+    [ -z $SUDO_UID ] || uid=$SUDO_UID:$SUDO_GID
+
+    local cmd="
+mkdir -p ${JUJU_HOME}/${HOME}
+mkdir -p /run/lock
+${main_cmd}
+"
+
+    JUJU_ENV=1 ${CHROOT} $JUJU_HOME /usr/bin/bash -c "${cmd}"
+
+    # The ownership of the files in JuJu is assigned to the real user
+    [ -z $uid ] || ${CHOWN} -R ${uid} ${JUJU_HOME}
 }
 
 function _run_proot(){
@@ -239,7 +247,7 @@ function _check_package(){
 
 function build_image_juju(){
 # The function must runs on ArchLinux with non-root privileges.
-    [ "$(id -u)" == "0" ] && \
+    [ "$(${ID})" == "0" ] && \
         die "You cannot build with root privileges."
 
     _check_package arch-install-scripts
diff --git a/tests/test_core.sh b/tests/test_core.sh
index 6421d09..f84b17d 100755
--- a/tests/test_core.sh
+++ b/tests/test_core.sh
@@ -102,14 +102,21 @@ function test_setup_from_file_juju_with_absolute_path(){
 function test_run_juju_as_root(){
     install_mini_juju
     CHROOT="sudo $CHROOT"
-    SH="type -t type"
+    CHOWN="sudo $CHOWN"
+    SH=("type" "-t" "type")
     local output=$(run_juju_as_root)
     is_equal $output "builtin" || return 1
     local output=$(run_juju_as_root pwd)
     is_equal $output "/" || return 1
     run_juju_as_root "[ -e /run/lock ]"
     is_equal $? 0 || return 1
-    [ -e $JUJU_HOME/${HOME} ] || return 1
+    run_juju_as_root "[ -e $HOME ]"
+    is_equal $? 0 || return 1
+
+    # test that normal user has ownership of the files created by root
+    run_juju_as_root "touch /a_root_file"
+    local output=$(run_juju_as_root "stat -c '%u' /a_root_file")
+    is_equal $output "$UID" || return 1
 }
 
 function test_run_juju_as_user(){