diff --git a/src/Parser.zig b/src/Parser.zig
index 818abda..40d99fe 100644
--- a/src/Parser.zig
+++ b/src/Parser.zig
@@ -82,8 +82,10 @@ pub fn init(gpa: std.mem.Allocator, arena: std.mem.Allocator, io: std.Io, cflags
     driver.nostdlibinc = true;
     driver.nobuiltininc = true;
 
-    // Configure include search order from the bundled sysroot.
-    try include_paths.addZigCcImplicitIncludes(driver.comp, resource_dir_dupe);
+    // Stage bundled-sysroot search paths in `driver.includes`; user `-I` flags
+    // from `parseArgs` will join the same list and a single `initSearchPath`
+    // call below commits them all.
+    try include_paths.addZigCcImplicitIncludes(driver, resource_dir_dupe);
 
     // Add compatibility macros for LLVM/Clang 18+ headers.
     // __building_module(x) is a Clang builtin that returns 0 unless building a specific
@@ -93,9 +95,11 @@ pub fn init(gpa: std.mem.Allocator, arena: std.mem.Allocator, io: std.Io, cflags
         \\#define __building_module(x) 0
         \\
     );
-    // We call buildUserMacros before generateBuiltinMacros as calling parseArgs will
-    // update the driver state
+    // buildUserMacros runs parseArgs, which appends user includes to
+    // `driver.includes` and updates driver state, so it must come before
+    // initSearchPath and generateBuiltinMacros.
     const user_macros = try buildUserMacros(toolchain, cflags, gpa);
+    try driver.comp.initSearchPath(driver.includes.items, driver.verbose_search_path);
     const builtin_source = try driver.comp.generateBuiltinMacros(driver.system_defines);
 
     return .{
@@ -146,8 +150,8 @@ pub fn deinit(p: *Parser) void {
     var diag: *aro.Diagnostics = p.diagnostics;
 
     p.toolchain.deinit();
-    comp.deinit();
     driver.deinit();
+    comp.deinit();
     diag.deinit();
 
     p.gpa.destroy(comp);
diff --git a/src/include_paths.zig b/src/include_paths.zig
index 572fe75..5cb47af 100644
--- a/src/include_paths.zig
+++ b/src/include_paths.zig
@@ -6,7 +6,10 @@
 const aro = @import("aro");
 const std = @import("std");
 
-/// Configure the compilation's include search paths using the bundled sysroot.
+/// Append the bundled-sysroot include paths to `driver.includes`.
+/// The caller commits the merged list (system + user) to the compilation
+/// via a single `initSearchPath` call, mirroring aro's normal driver flow.
+///
 /// The bundled sysroot lives under `resource_dir/lib/...`. We add directories
 /// in the same order that `zig cc -E -v` reports, except we intentionally omit
 /// /usr/local/include and /usr/include to keep absolution self-contained:
@@ -15,18 +18,16 @@ const std = @import("std");
 ///   3. <prefix>/lib/libc/include/generic-<abi-family> (generic libc headers)
 ///   4. <prefix>/lib/libc/include/<arch>-<os>-any (arch+os wildcards)
 ///   5. <prefix>/lib/libc/include/any-<os>-any (os-only wildcards)
-pub fn addZigCcImplicitIncludes(comp: *aro.Compilation, resource_dir: []const u8) !void {
+pub fn addZigCcImplicitIncludes(driver: *aro.Driver, resource_dir: []const u8) !void {
+    const comp = driver.comp;
     const target = comp.target;
     const arch = target.cpu.arch;
     const os = target.os.tag;
     const abi = target.abi;
 
-    var includes: std.ArrayList(aro.Compilation.Include) = .empty;
-    defer includes.deinit(comp.gpa);
-
     // 1. Zig's compiler-provided headers (stddef.h, stdarg.h, etc.)
     const zig_lib_include = try std.fs.path.join(comp.arena, &.{ resource_dir, "lib", "include" });
-    try includes.append(comp.gpa, .{ .kind = .system, .path = zig_lib_include });
+    try driver.includes.append(comp.gpa, .{ .kind = .system, .path = zig_lib_include });
 
     const libc_include_base = try std.fs.path.join(comp.arena, &.{ resource_dir, "lib", "libc", "include" });
 
@@ -34,31 +35,30 @@ pub fn addZigCcImplicitIncludes(comp: *aro.Compilation, resource_dir: []const u8
     const target_subdir = try getTargetLibcSubdir(comp.arena, arch, os, abi);
     if (target_subdir) |subdir| {
         const target_include = try std.fs.path.join(comp.arena, &.{ libc_include_base, subdir });
-        try includes.append(comp.gpa, .{ .kind = .system, .path = target_include });
+        try driver.includes.append(comp.gpa, .{ .kind = .system, .path = target_include });
     }
 
     // 3. Generic libc headers based on ABI family (glibc, musl, etc.)
     const generic_subdir = getGenericLibcSubdir(abi);
     if (generic_subdir) |subdir| {
         const generic_include = try std.fs.path.join(comp.arena, &.{ libc_include_base, subdir });
-        try includes.append(comp.gpa, .{ .kind = .system, .path = generic_include });
+        try driver.includes.append(comp.gpa, .{ .kind = .system, .path = generic_include });
     }
 
     // 4. Architecture + OS wildcard headers (e.g., x86-linux-any)
     const arch_os_any = try getArchOsAnySubdir(comp.arena, arch, os);
     if (arch_os_any) |subdir| {
         const arch_os_include = try std.fs.path.join(comp.arena, &.{ libc_include_base, subdir });
-        try includes.append(comp.gpa, .{ .kind = .system, .path = arch_os_include });
+        try driver.includes.append(comp.gpa, .{ .kind = .system, .path = arch_os_include });
     }
 
     // 5. OS-only wildcard headers (e.g., any-linux-any)
     const any_os_any = try getAnyOsAnySubdir(comp.arena, os);
     if (any_os_any) |subdir| {
         const any_os_include = try std.fs.path.join(comp.arena, &.{ libc_include_base, subdir });
-        try includes.append(comp.gpa, .{ .kind = .system, .path = any_os_include });
+        try driver.includes.append(comp.gpa, .{ .kind = .system, .path = any_os_include });
     }
 
-    try comp.initSearchPath(includes.items, false);
     // Note: We intentionally do NOT add /usr/local/include or /usr/include.
     // absolution is self-contained and uses only the bundled headers from the
     // build-time copied sysroot. This ensures:
diff --git a/tests/user_include_path_resolution/inc/inner.h b/tests/user_include_path_resolution/inc/inner.h
new file mode 100644
index 0000000..db4e406
--- /dev/null
+++ b/tests/user_include_path_resolution/inc/inner.h
@@ -0,0 +1,6 @@
+#pragma once
+
+typedef struct {
+    int id;
+    int value;
+} inner_t;
diff --git a/tests/user_include_path_resolution/target.c b/tests/user_include_path_resolution/target.c
new file mode 100644
index 0000000..dce5076
--- /dev/null
+++ b/tests/user_include_path_resolution/target.c
@@ -0,0 +1,15 @@
+/* Regression test: user-supplied -I flags must reach the preprocessor's
+ * include search path.
+ *
+ * The header `inner.h` lives in a sibling subdirectory `inc/`, so the
+ * preprocessor cannot find it via the includer's directory alone — it
+ * MUST honour the `-I .../inc` flag passed via target.c.flags.
+ *
+ * This guards against a regression where Driver.parseArgs collected
+ * `-I/-isystem/-iquote/-idirafter` into `driver.includes` but the result
+ * was never committed to `comp.search_path`, leaving every user-supplied
+ * include path invisible to the preprocessor.
+ */
+#include "inner.h"
+
+inner_t global_state;
diff --git a/tests/user_include_path_resolution/target.c.flags b/tests/user_include_path_resolution/target.c.flags
new file mode 100644
index 0000000..146d70c
--- /dev/null
+++ b/tests/user_include_path_resolution/target.c.flags
@@ -0,0 +1,4 @@
+# Force the preprocessor to rely on a user-supplied include path: the
+# header `inner.h` only exists under tests/user_include_path_resolution/inc/.
+-I
+tests/user_include_path_resolution/inc
diff --git a/tests/user_include_path_resolution/target.c.zon b/tests/user_include_path_resolution/target.c.zon
new file mode 100644
index 0000000..d6f7f33
--- /dev/null
+++ b/tests/user_include_path_resolution/target.c.zon
@@ -0,0 +1,22 @@
+.{.{
+    .name = "global_state",
+    .source_file = "tests/user_include_path_resolution/target.c",
+    .size_bytes = 8,
+    .is_static = false,
+    .dims = .{},
+    .fields = .{ .{
+        .name = ".id",
+        .offset_bits = 0,
+        .bit_width = 32,
+        .dims = .{},
+        .is_padding = false,
+        .domain = .top,
+    }, .{
+        .name = ".value",
+        .offset_bits = 32,
+        .bit_width = 32,
+        .dims = .{},
+        .is_padding = false,
+        .domain = .top,
+    } },
+}}