diff --git a/master_changes.md b/master_changes.md
index bc2c04e23cc..d63569fc5b6 100644
--- a/master_changes.md
+++ b/master_changes.md
@@ -20,6 +20,7 @@ users)
 
 ## Init
   * [BUG] Fix the detection of `ZDOTDIR` when using `zsh` [#6299 @acasta-yhliu - fix #6281]
+  * Remove `ocaml-system` from the list of default compilers [#6307 @kit-ty-kate - fix #3509]
 
 ## Config report
 
diff --git a/src/client/opamInitDefaults.ml b/src/client/opamInitDefaults.ml
index 0a9e5d6d4ef..75f7358733e 100644
--- a/src/client/opamInitDefaults.ml
+++ b/src/client/opamInitDefaults.ml
@@ -19,12 +19,8 @@ let repository_url = {
 }
 
 let default_compiler =
-  OpamFormula.ors [
-    OpamFormula.Atom (OpamPackage.Name.of_string "ocaml-system",
-                      OpamFormula.Empty);
-    OpamFormula.Atom (OpamPackage.Name.of_string "ocaml-base-compiler",
-                      OpamFormula.Empty);
-  ]
+  OpamFormula.Atom (OpamPackage.Name.of_string "ocaml-base-compiler",
+                    OpamFormula.Empty)
 
 let default_invariant =
   OpamFormula.Atom
diff --git a/tests/reftests/init.test b/tests/reftests/init.test
index d02ba15037f..bdcf2a0b7bf 100644
--- a/tests/reftests/init.test
+++ b/tests/reftests/init.test
@@ -116,36 +116,23 @@ Configuring from ${BASEDIR}/opamrc and then from built-in defaults.
 <><> Fetching repository information ><><><><><><><><><><><><><><><><><><><><><>
 [default] Initialised
 
-<><> Creating initial switch 'default' (invariant ["ocaml" {>= "4.05.0"}] - initially with ocaml-system)
+<><> Creating initial switch 'default' (invariant ["ocaml" {>= "4.05.0"}] - initially with ocaml-base-compiler)
 
 <><> Installing new switch packages <><><><><><><><><><><><><><><><><><><><><><>
 Switch invariant: ["ocaml" {>= "4.05.0"}]
 
 <><> Processing actions <><><><><><><><><><><><><><><><><><><><><><><><><><><><>
--> installed ocaml-system.4.07.0
--> installed ocaml.4.07.0
+-> installed ocaml-base-compiler.4.10.0
+-> installed ocaml.4.10.0
 Done.
 ### opam switch invariant
 ["ocaml" {>= "4.05.0"}]
 ### opam upgrade
-Everything as up-to-date as possible (run with --verbose to show unavailable upgrades).
-However, you may "opam upgrade" these packages explicitly at these versions (e.g. "opam upgrade ocaml.4.10.0"), which will ask permission to downgrade or uninstall the conflicting packages.
+Already up-to-date.
 Nothing to do.
 ### opam upgrade ocaml
-The following actions will be performed:
-=== remove 1 package
-  - remove  ocaml-system        4.07.0           [conflicts with ocaml-base-compiler]
-=== upgrade 1 package
-  - upgrade ocaml               4.07.0 to 4.10.0
-=== install 1 package
-  - install ocaml-base-compiler 4.10.0           [required by ocaml]
-
-<><> Processing actions <><><><><><><><><><><><><><><><><><><><><><><><><><><><>
--> removed   ocaml.4.07.0
--> removed   ocaml-system.4.07.0
--> installed ocaml-base-compiler.4.10.0
--> installed ocaml.4.10.0
-Done.
+Already up-to-date.
+Nothing to do.
 ### : Init with config file :
 ### :: default setup ::
 ### rm -rf $OPAMROOT
@@ -155,7 +142,7 @@ No configuration file found, using built-in defaults.
 <><> Fetching repository information ><><><><><><><><><><><><><><><><><><><><><>
 [default] Initialised
 ### opam-cat $OPAMROOT/config | 'opam-root-version: "${OPAMROOTVERSION}"' -> 'opam-root-version: current' | grep -v sys-pkg-manager-cmd | grep -v global-variables | grep -v eval-variables:
-default-compiler: ["ocaml-system" "ocaml-base-compiler"]
+default-compiler: ["ocaml-base-compiler"]
 default-invariant: ["ocaml" {>= "4.05.0"}]
 depext: true
 depext-cannot-install: false