diff --git a/HISTORY.rst b/HISTORY.rst
index f66848c2..657a429b 100644
--- a/HISTORY.rst
+++ b/HISTORY.rst
@@ -22,6 +22,8 @@ test-driven methodologies, and modern toolchains for unrivaled success.
 6.1.19 (2025-??-??)
 ~~~~~~~~~~~~~~~~~~~
 
+* Fixed a regression issue where custom build flags were not properly reflected in the `compile_commands.json <https://docs.platformio.org/en/latest/integration/compile_commands.html>`__ file, ensuring accurate compilation database generation
+
 6.1.18 (2025-03-11)
 ~~~~~~~~~~~~~~~~~~~
 
diff --git a/platformio/builder/tools/piobuild.py b/platformio/builder/tools/piobuild.py
index e1a310bd..8ef2522c 100644
--- a/platformio/builder/tools/piobuild.py
+++ b/platformio/builder/tools/piobuild.py
@@ -58,8 +58,8 @@ def GetBuildType(env):
 
 
 def BuildProgram(env):
-    env.ProcessCompileDbToolchainOption()
     env.ProcessProgramDeps()
+    env.ProcessCompileDbToolchainOption()
     env.ProcessProjectDeps()
 
     # append into the beginning a main LD script
@@ -91,26 +91,6 @@ def BuildProgram(env):
     return program
 
 
-def ProcessCompileDbToolchainOption(env):
-    if "compiledb" not in COMMAND_LINE_TARGETS:
-        return
-    # Resolve absolute path of toolchain
-    for cmd in ("CC", "CXX", "AS"):
-        if cmd not in env:
-            continue
-        if os.path.isabs(env[cmd]) or '"' in env[cmd]:
-            continue
-        env[cmd] = where_is_program(env.subst("$%s" % cmd), env.subst("${ENV['PATH']}"))
-        if " " in env[cmd]:  # issue #4998: Space in compilator path
-            env[cmd] = f'"{env[cmd]}"'
-
-    if env.get("COMPILATIONDB_INCLUDE_TOOLCHAIN"):
-        print("Warning! `COMPILATIONDB_INCLUDE_TOOLCHAIN` is scoping")
-        for scope, includes in env.DumpIntegrationIncludes().items():
-            if scope in ("toolchain",):
-                env.Append(CPPPATH=includes)
-
-
 def ProcessProgramDeps(env):
     def _append_pio_macros():
         core_version = pepver_to_semver(__version__)
@@ -148,6 +128,27 @@ def ProcessProgramDeps(env):
     env.ProcessUnFlags(env.get("BUILD_UNFLAGS"))
 
 
+def ProcessCompileDbToolchainOption(env):
+    if "compiledb" not in COMMAND_LINE_TARGETS:
+        return
+
+    # Resolve absolute path of toolchain
+    for cmd in ("CC", "CXX", "AS"):
+        if cmd not in env:
+            continue
+        if os.path.isabs(env[cmd]) or '"' in env[cmd]:
+            continue
+        env[cmd] = where_is_program(env.subst("$%s" % cmd), env.subst("${ENV['PATH']}"))
+        if " " in env[cmd]:  # issue #4998: Space in compilator path
+            env[cmd] = f'"{env[cmd]}"'
+
+    if env.get("COMPILATIONDB_INCLUDE_TOOLCHAIN"):
+        print("Warning! `COMPILATIONDB_INCLUDE_TOOLCHAIN` is scoping")
+        for scope, includes in env.DumpIntegrationIncludes().items():
+            if scope in ("toolchain",):
+                env.Append(CPPPATH=includes)
+
+
 def ProcessProjectDeps(env):
     plb = env.ConfigureProjectLibBuilder()