diff --git a/.mise/README.md b/.ci/mise/README.md
similarity index 63%
rename from .mise/README.md
rename to .ci/mise/README.md
index 215b7142..e45831c4 100644
--- a/.mise/README.md
+++ b/.ci/mise/README.md
@@ -11,12 +11,12 @@ of Bazel and CodeChecker.
 Files
 -----
 
-File               | Description
------------------- | -----------
-.mise/config.toml  | Mise configuration, contains tools and tasks
-.mise/init.sh      | Source this script to install and init mise
-.mise/run.sh       | Run this script to run mise tasks from CI
-.mise/print-env.sh | Utility script to show current versions of tools
+File                  | Description
+--------------------- | -----------
+.ci/mise/config.toml  | Mise configuration, contains tools and tasks
+.ci/mise/init.sh      | Source this script to install and init mise
+.ci/mise/run.sh       | Run this script to run mise tasks from CI
+.ci/mise/print-env.sh | Utility script to show current versions of tools
 
 
 How to use
@@ -26,15 +26,20 @@ How to use
 
 To install and initialize mise just run the following:
 ```bash
-source .mise/init.sh
+source .ci/mise/init.sh
 ```
 
 This script automatically downloads, installs, and runs `mise install`
 to install all default tools.
 
+> [!IMPORTANT]
+> You must source the `init.sh` script (not just execute it) as it sets the
+> `MISE_CONFIG_FILE` environment variable to point to the custom config location
+> at `.ci/mise/config.toml`.
+
 Note that once installed in your local environment mise and tools will
 remain in the cache (`~/.local/share/mise/`), so next time if you run
-`source .mise/init.sh` again it will take no time.
+`source .ci/mise/init.sh` again it will take no time.
 
 ### After installation
 
@@ -49,7 +54,7 @@ And execute tasks and tests in the environment controlled by mise.
 
 ### Run tests
 
-In `.mise` directory you can find `config.toml` file which describes
+In `.ci/mise` directory you can find `config.toml` file which describes
 all default tools and some test tasks - you can run them manually.  
 Or use wrapper script which basically runs initialization and then
 executes `mise run` command.
@@ -57,10 +62,10 @@ executes `mise run` command.
 For example, you can run unit tests with Bazel 7 and CodeChecker 6.25
 using `pytest` with maximum verbosity:
 ```bash
-.mise/run.sh test:7-25 test/unit -vvv
+.ci/mise/run.sh test:7-25 test/unit -vvv
 ```
 
-Note that `.mise/run.sh` script is just a convenience for CI (Continuous Integration).
+Note that `.ci/mise/run.sh` script is just a convenience for CI (Continuous Integration).
 
 ### Uninstall
 
diff --git a/.mise/config.toml b/.ci/mise/config.toml
similarity index 98%
rename from .mise/config.toml
rename to .ci/mise/config.toml
index 40c10b28..6691f135 100644
--- a/.mise/config.toml
+++ b/.ci/mise/config.toml
@@ -21,7 +21,7 @@ experimental = true
 
 
 [vars]
-run = ".mise/print-env.sh -vvv && pytest"
+run = ".ci/mise/print-env.sh -vvv && pytest"
 
 
 [tasks."install:bazel-6"]
diff --git a/.mise/init.sh b/.ci/mise/init.sh
similarity index 96%
rename from .mise/init.sh
rename to .ci/mise/init.sh
index 6f31e7c2..4a7965bf 100644
--- a/.mise/init.sh
+++ b/.ci/mise/init.sh
@@ -24,6 +24,7 @@ fi
 mise trust --quiet
 mise version
 export MISE_CONDA_CONCURRENCY=1
+export MISE_CONFIG_FILE=".ci/mise/config.toml"
 mise install || mise install
 mise reshim
 
diff --git a/.mise/print-env.sh b/.ci/mise/print-env.sh
similarity index 100%
rename from .mise/print-env.sh
rename to .ci/mise/print-env.sh
diff --git a/.mise/run.sh b/.ci/mise/run.sh
similarity index 100%
rename from .mise/run.sh
rename to .ci/mise/run.sh
diff --git a/.github/workflows/mise.yaml b/.github/workflows/mise.yaml
index f39c504d..3893fdda 100644
--- a/.github/workflows/mise.yaml
+++ b/.github/workflows/mise.yaml
@@ -60,12 +60,12 @@ jobs:
 
       - name: Install and init mise
         run: |
-          source .mise/init.sh
+          source .ci/mise/init.sh
 
       - name: Install all versions
         run: |
-          .mise/run.sh install
+          .ci/mise/run.sh install
 
       - name: Run Mise tests
         run: |
-          .mise/run.sh ${{ inputs.arguments }}
+          .ci/mise/run.sh ${{ inputs.arguments }}