diff --git a/csharp/ql/integration-tests/windows/subst/code/Program.cs b/csharp/ql/integration-tests/windows/subst/code/Program.cs
new file mode 100644
index 000000000000..b5fc9827b28b
--- /dev/null
+++ b/csharp/ql/integration-tests/windows/subst/code/Program.cs
@@ -0,0 +1,4 @@
+class Program
+{
+    static void Main() {}
+}
diff --git a/csharp/ql/integration-tests/windows/subst/code/dotnet_build.csproj b/csharp/ql/integration-tests/windows/subst/code/dotnet_build.csproj
new file mode 100644
index 000000000000..694035b3acd5
--- /dev/null
+++ b/csharp/ql/integration-tests/windows/subst/code/dotnet_build.csproj
@@ -0,0 +1,10 @@
+<Project Sdk="Microsoft.NET.Sdk">
+
+  <PropertyGroup>
+    <OutputType>Exe</OutputType>
+    <TargetFramework>net9.0</TargetFramework>
+    <ImplicitUsings>enable</ImplicitUsings>
+    <Nullable>enable</Nullable>
+  </PropertyGroup>
+
+</Project>
diff --git a/csharp/ql/integration-tests/windows/subst/code/global.json b/csharp/ql/integration-tests/windows/subst/code/global.json
new file mode 100644
index 000000000000..9ceca3771e69
--- /dev/null
+++ b/csharp/ql/integration-tests/windows/subst/code/global.json
@@ -0,0 +1,5 @@
+{
+    "sdk": {
+        "version": "9.0.201"
+    }
+}
diff --git a/csharp/ql/integration-tests/windows/subst/file.expected b/csharp/ql/integration-tests/windows/subst/file.expected
new file mode 100644
index 000000000000..6421dce41212
--- /dev/null
+++ b/csharp/ql/integration-tests/windows/subst/file.expected
@@ -0,0 +1,8 @@
+| code/Program.cs:0:0:0:0 | code/Program.cs |  |
+| code/obj/Debug/net9.0/.NETCoreApp,Version=v9.0.AssemblyAttributes.cs:0:0:0:0 | code/obj/Debug/net9.0/.NETCoreApp,Version=v9.0.AssemblyAttributes.cs |  |
+| code/obj/Debug/net9.0/dotnet_build.AssemblyInfo.cs:0:0:0:0 | code/obj/Debug/net9.0/dotnet_build.AssemblyInfo.cs |  |
+| code/obj/Debug/net9.0/dotnet_build.GlobalUsings.g.cs:0:0:0:0 | code/obj/Debug/net9.0/dotnet_build.GlobalUsings.g.cs |  |
+| code/obj/Debug/net9.0/dotnet_build.dll:0:0:0:0 | code/obj/Debug/net9.0/dotnet_build.dll |  |
+| file://:0:0:0:0 |  |  |
+| file://Z:/dotnet_build.csproj:0:0:0:0 | Z:/dotnet_build.csproj | relative |
+| file://Z:/obj/dotnet_build.csproj.nuget.g.props:0:0:0:0 | Z:/obj/dotnet_build.csproj.nuget.g.props | relative |
diff --git a/csharp/ql/integration-tests/windows/subst/file.ql b/csharp/ql/integration-tests/windows/subst/file.ql
new file mode 100644
index 000000000000..43cc4a13fdc5
--- /dev/null
+++ b/csharp/ql/integration-tests/windows/subst/file.ql
@@ -0,0 +1,7 @@
+import csharp
+
+from File f, string relative
+where
+  not f.getURL().matches("file://C:/Program Files/%") and
+  if exists(f.getRelativePath()) then relative = "relative" else relative = ""
+select f, relative
diff --git a/csharp/ql/integration-tests/windows/subst/test.py b/csharp/ql/integration-tests/windows/subst/test.py
new file mode 100644
index 000000000000..8fbb3201cd4f
--- /dev/null
+++ b/csharp/ql/integration-tests/windows/subst/test.py
@@ -0,0 +1,7 @@
+import runs_on
+
+
+@runs_on.windows
+def test(codeql, csharp, cwd, subst_drive):
+    drive = subst_drive(cwd / "code")
+    codeql.database.create(source_root=drive)
diff --git a/go/ql/integration-tests/subst/code/main.go b/go/ql/integration-tests/subst/code/main.go
new file mode 100644
index 000000000000..38dd16da61ac
--- /dev/null
+++ b/go/ql/integration-tests/subst/code/main.go
@@ -0,0 +1,3 @@
+package main
+
+func main() {}
diff --git a/go/ql/integration-tests/subst/file.expected b/go/ql/integration-tests/subst/file.expected
new file mode 100644
index 000000000000..b86b34681e44
--- /dev/null
+++ b/go/ql/integration-tests/subst/file.expected
@@ -0,0 +1 @@
+| file://Z:/main.go:0:0:0:0 | Z:/main.go | relative |
diff --git a/go/ql/integration-tests/subst/file.ql b/go/ql/integration-tests/subst/file.ql
new file mode 100644
index 000000000000..0abcfdc784ad
--- /dev/null
+++ b/go/ql/integration-tests/subst/file.ql
@@ -0,0 +1,5 @@
+import go
+
+from File f, string relative
+where if exists(f.getRelativePath()) then relative = "relative" else relative = ""
+select f, relative
diff --git a/go/ql/integration-tests/subst/test.py b/go/ql/integration-tests/subst/test.py
new file mode 100644
index 000000000000..2fafe00927af
--- /dev/null
+++ b/go/ql/integration-tests/subst/test.py
@@ -0,0 +1,7 @@
+import runs_on
+
+
+@runs_on.windows
+def test(codeql, go, cwd, subst_drive):
+    drive = subst_drive(cwd / "code")
+    codeql.database.create(command="go build main.go", source_root=drive)
diff --git a/java/ql/integration-tests/java/subst/code/test1.java b/java/ql/integration-tests/java/subst/code/test1.java
new file mode 100644
index 000000000000..4bdfe39fca7a
--- /dev/null
+++ b/java/ql/integration-tests/java/subst/code/test1.java
@@ -0,0 +1,4 @@
+class test {
+  public static void main(String[] args) {
+  }
+}
diff --git a/java/ql/integration-tests/java/subst/code/test2.kt b/java/ql/integration-tests/java/subst/code/test2.kt
new file mode 100644
index 000000000000..d44a1616c018
--- /dev/null
+++ b/java/ql/integration-tests/java/subst/code/test2.kt
@@ -0,0 +1 @@
+fun main() {}
diff --git a/java/ql/integration-tests/java/subst/file.expected b/java/ql/integration-tests/java/subst/file.expected
new file mode 100644
index 000000000000..cca997b1a06c
--- /dev/null
+++ b/java/ql/integration-tests/java/subst/file.expected
@@ -0,0 +1,5 @@
+| file://:0:0:0:0 |  |  |
+| file://:0:0:0:0 |  |  |
+| file://Z:/test1.java:0:0:0:0 | test1 | relative |
+| file://Z:/test2.kt:0:0:0:0 | test2 | relative |
+| file://Z:/test.class:0:0:0:0 | test | relative |
diff --git a/java/ql/integration-tests/java/subst/file.ql b/java/ql/integration-tests/java/subst/file.ql
new file mode 100644
index 000000000000..504db61890ce
--- /dev/null
+++ b/java/ql/integration-tests/java/subst/file.ql
@@ -0,0 +1,9 @@
+import java
+
+from File f, string relative
+where
+  not f.getURL().matches("file:///modules/%") and
+  not f.getURL().matches("file:///!unknown-binary-location/kotlin/%") and
+  not f.getURL().matches("%/semmle-code/semmle-code/%") and
+  if exists(f.getRelativePath()) then relative = "relative" else relative = ""
+select f, relative
diff --git a/java/ql/integration-tests/java/subst/test.py b/java/ql/integration-tests/java/subst/test.py
new file mode 100644
index 000000000000..5c162ab08d9b
--- /dev/null
+++ b/java/ql/integration-tests/java/subst/test.py
@@ -0,0 +1,7 @@
+import runs_on
+
+
+@runs_on.windows
+def test(codeql, java, cwd, subst_drive):
+    drive = subst_drive(cwd / "code")
+    codeql.database.create(command=["javac test1.java", "kotlinc test2.kt"], source_root=drive)
diff --git a/javascript/ql/integration-tests/subst/code/main.js b/javascript/ql/integration-tests/subst/code/main.js
new file mode 100644
index 000000000000..8dbc3ac70473
--- /dev/null
+++ b/javascript/ql/integration-tests/subst/code/main.js
@@ -0,0 +1 @@
+function interesting() { }
diff --git a/javascript/ql/integration-tests/subst/code/test.ts b/javascript/ql/integration-tests/subst/code/test.ts
new file mode 100644
index 000000000000..573541ac9702
--- /dev/null
+++ b/javascript/ql/integration-tests/subst/code/test.ts
@@ -0,0 +1 @@
+0
diff --git a/javascript/ql/integration-tests/subst/file.expected b/javascript/ql/integration-tests/subst/file.expected
new file mode 100644
index 000000000000..10416eb5e733
--- /dev/null
+++ b/javascript/ql/integration-tests/subst/file.expected
@@ -0,0 +1,2 @@
+| file://Z:/main.js:0:0:0:0 | Z:/main.js | relative |
+| file://Z:/test.ts:0:0:0:0 | Z:/test.ts | relative |
diff --git a/javascript/ql/integration-tests/subst/file.ql b/javascript/ql/integration-tests/subst/file.ql
new file mode 100644
index 000000000000..d4b1f330d42f
--- /dev/null
+++ b/javascript/ql/integration-tests/subst/file.ql
@@ -0,0 +1,7 @@
+import javascript
+
+from File f, string relative
+where
+  not f.getURL().matches("%/semmle-code/semmle-code/%") and
+  if exists(f.getRelativePath()) then relative = "relative" else relative = ""
+select f, relative
diff --git a/javascript/ql/integration-tests/subst/test.py b/javascript/ql/integration-tests/subst/test.py
new file mode 100644
index 000000000000..98b1c76d517c
--- /dev/null
+++ b/javascript/ql/integration-tests/subst/test.py
@@ -0,0 +1,7 @@
+import runs_on
+
+
+@runs_on.windows
+def test(codeql, javascript, cwd, subst_drive):
+    drive = subst_drive(cwd / "code")
+    codeql.database.create(source_root=drive)
diff --git a/python/ql/integration-tests/subst/code/main.py b/python/ql/integration-tests/subst/code/main.py
new file mode 100644
index 000000000000..3e978a7aa9ef
--- /dev/null
+++ b/python/ql/integration-tests/subst/code/main.py
@@ -0,0 +1 @@
+print(0)
diff --git a/python/ql/integration-tests/subst/file.expected b/python/ql/integration-tests/subst/file.expected
new file mode 100644
index 000000000000..1bc4d03914a1
--- /dev/null
+++ b/python/ql/integration-tests/subst/file.expected
@@ -0,0 +1 @@
+| code/main.py:0:0:0:0 | code/main.py |  |
diff --git a/python/ql/integration-tests/subst/file.ql b/python/ql/integration-tests/subst/file.ql
new file mode 100644
index 000000000000..779bbe981104
--- /dev/null
+++ b/python/ql/integration-tests/subst/file.ql
@@ -0,0 +1,5 @@
+import python
+
+from File f, string relative
+where if exists(f.getRelativePath()) then relative = "relative" else relative = ""
+select f, relative
diff --git a/python/ql/integration-tests/subst/test.py b/python/ql/integration-tests/subst/test.py
new file mode 100644
index 000000000000..627810a6dc1e
--- /dev/null
+++ b/python/ql/integration-tests/subst/test.py
@@ -0,0 +1,7 @@
+import runs_on
+
+
+@runs_on.windows
+def test(codeql, python, cwd, subst_drive):
+    drive = subst_drive(cwd / "code")
+    codeql.database.create(source_root=drive)
diff --git a/ruby/ql/integration-tests/subst/code/test.rb b/ruby/ql/integration-tests/subst/code/test.rb
new file mode 100644
index 000000000000..573541ac9702
--- /dev/null
+++ b/ruby/ql/integration-tests/subst/code/test.rb
@@ -0,0 +1 @@
+0
diff --git a/ruby/ql/integration-tests/subst/file.expected b/ruby/ql/integration-tests/subst/file.expected
new file mode 100644
index 000000000000..47b324fea9e9
--- /dev/null
+++ b/ruby/ql/integration-tests/subst/file.expected
@@ -0,0 +1,2 @@
+| code/test.rb:0:0:0:0 | code/test.rb |  |
+| file://:0:0:0:0 |  |  |
diff --git a/ruby/ql/integration-tests/subst/file.ql b/ruby/ql/integration-tests/subst/file.ql
new file mode 100644
index 000000000000..55944637191d
--- /dev/null
+++ b/ruby/ql/integration-tests/subst/file.ql
@@ -0,0 +1,5 @@
+import ruby
+
+from File f, string relative
+where if exists(f.getRelativePath()) then relative = "relative" else relative = ""
+select f, relative
diff --git a/ruby/ql/integration-tests/subst/test.py b/ruby/ql/integration-tests/subst/test.py
new file mode 100644
index 000000000000..74ff84ce4a5b
--- /dev/null
+++ b/ruby/ql/integration-tests/subst/test.py
@@ -0,0 +1,7 @@
+import runs_on
+
+
+@runs_on.windows
+def test(codeql, ruby, cwd, subst_drive):
+    drive = subst_drive(cwd / "code")
+    codeql.database.create(source_root=drive)
diff --git a/rust/ql/integration-tests/subst/code/test.rs b/rust/ql/integration-tests/subst/code/test.rs
new file mode 100644
index 000000000000..f328e4d9d04c
--- /dev/null
+++ b/rust/ql/integration-tests/subst/code/test.rs
@@ -0,0 +1 @@
+fn main() {}
diff --git a/rust/ql/integration-tests/subst/file.expected b/rust/ql/integration-tests/subst/file.expected
new file mode 100644
index 000000000000..c1ff73337f2a
--- /dev/null
+++ b/rust/ql/integration-tests/subst/file.expected
@@ -0,0 +1,2 @@
+| code/test.rs:0:0:0:0 | code/test.rs |  |
+| file://:0:0:0:0 |  |  |
diff --git a/rust/ql/integration-tests/subst/file.ql b/rust/ql/integration-tests/subst/file.ql
new file mode 100644
index 000000000000..3fc437fd6b7f
--- /dev/null
+++ b/rust/ql/integration-tests/subst/file.ql
@@ -0,0 +1,7 @@
+import rust
+
+from File f, string relative
+where
+  not f.getURL().matches("%/semmle-code/semmle-code/%") and
+  if exists(f.getRelativePath()) then relative = "relative" else relative = ""
+select f, relative
diff --git a/rust/ql/integration-tests/subst/test.py b/rust/ql/integration-tests/subst/test.py
new file mode 100644
index 000000000000..6d49adcab170
--- /dev/null
+++ b/rust/ql/integration-tests/subst/test.py
@@ -0,0 +1,7 @@
+import runs_on
+
+
+@runs_on.windows
+def test(codeql, rust, cwd, subst_drive):
+    drive = subst_drive(cwd / "code")
+    codeql.database.create(source_root=drive)