diff --git a/.appveyor.yml b/.appveyor.yml
index 8f0d49a9d67f..dc431ded5018 100644
--- a/.appveyor.yml
+++ b/.appveyor.yml
@@ -1,4 +1,4 @@
-version: 4.0.0.{build}
+version: 4.0.0.99.{build}
 
 image: Visual Studio 2015
 platform: x64
diff --git a/R-package/configure b/R-package/configure
index f9f96c84e6e7..867ef2d395a6 100755
--- a/R-package/configure
+++ b/R-package/configure
@@ -1,6 +1,6 @@
 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.71 for lightgbm 4.0.0.
+# Generated by GNU Autoconf 2.71 for lightgbm 4.0.0.99.
 #
 #
 # Copyright (C) 1992-1996, 1998-2017, 2020-2021 Free Software Foundation,
@@ -607,8 +607,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='lightgbm'
 PACKAGE_TARNAME='lightgbm'
-PACKAGE_VERSION='4.0.0'
-PACKAGE_STRING='lightgbm 4.0.0'
+PACKAGE_VERSION='4.0.0.99'
+PACKAGE_STRING='lightgbm 4.0.0.99'
 PACKAGE_BUGREPORT=''
 PACKAGE_URL=''
 
@@ -1211,7 +1211,7 @@ if test "$ac_init_help" = "long"; then
   # Omit some internal or obsolete options to make the list less imposing.
   # This message is too long to be a string in the A/UX 3.1 sh.
   cat <<_ACEOF
-\`configure' configures lightgbm 4.0.0 to adapt to many kinds of systems.
+\`configure' configures lightgbm 4.0.0.99 to adapt to many kinds of systems.
 
 Usage: $0 [OPTION]... [VAR=VALUE]...
 
@@ -1273,7 +1273,7 @@ fi
 
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of lightgbm 4.0.0:";;
+     short | recursive ) echo "Configuration of lightgbm 4.0.0.99:";;
    esac
   cat <<\_ACEOF
 
@@ -1341,7 +1341,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-lightgbm configure 4.0.0
+lightgbm configure 4.0.0.99
 generated by GNU Autoconf 2.71
 
 Copyright (C) 2021 Free Software Foundation, Inc.
@@ -1378,7 +1378,7 @@ cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
 
-It was created by lightgbm $as_me 4.0.0, which was
+It was created by lightgbm $as_me 4.0.0.99, which was
 generated by GNU Autoconf 2.71.  Invocation command line was
 
   $ $0$ac_configure_args_raw
@@ -2454,7 +2454,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 # report actual input values of CONFIG_FILES etc. instead of their
 # values after options handling.
 ac_log="
-This file was extended by lightgbm $as_me 4.0.0, which was
+This file was extended by lightgbm $as_me 4.0.0.99, which was
 generated by GNU Autoconf 2.71.  Invocation command line was
 
   CONFIG_FILES    = $CONFIG_FILES
@@ -2509,7 +2509,7 @@ ac_cs_config_escaped=`printf "%s\n" "$ac_cs_config" | sed "s/^ //; s/'/'\\\\\\\\
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config='$ac_cs_config_escaped'
 ac_cs_version="\\
-lightgbm config.status 4.0.0
+lightgbm config.status 4.0.0.99
 configured by $0, generated by GNU Autoconf 2.71,
   with options \\"\$ac_cs_config\\"
 
diff --git a/R-package/pkgdown/_pkgdown.yml b/R-package/pkgdown/_pkgdown.yml
index ca4a84a5d045..233a31f0ead9 100644
--- a/R-package/pkgdown/_pkgdown.yml
+++ b/R-package/pkgdown/_pkgdown.yml
@@ -14,7 +14,7 @@ repo:
     user: https://github.com/
 
 development:
-  mode: release
+  mode: unreleased
 
 authors:
   Yu Shi:
diff --git a/VERSION.txt b/VERSION.txt
index fcdb2e109f68..200681852af8 100644
--- a/VERSION.txt
+++ b/VERSION.txt
@@ -1 +1 @@
-4.0.0
+4.0.0.99
diff --git a/python-package/pyproject.toml b/python-package/pyproject.toml
index 600a92566ea1..d3ff28286bb9 100644
--- a/python-package/pyproject.toml
+++ b/python-package/pyproject.toml
@@ -29,7 +29,7 @@ maintainers = [
 name = "lightgbm"
 readme = "README.rst"
 requires-python = ">=3.6"
-version = "4.0.0"
+version = "4.0.0.99"
 
 [project.optional-dependencies]
 dask = [