diff --git a/ChangeLog.d/check-config.txt b/ChangeLog.d/check-config.txt
new file mode 100644
index 000000000..8570a1175
--- /dev/null
+++ b/ChangeLog.d/check-config.txt
@@ -0,0 +1,9 @@
+Changes
+   * Warn if mbedtls/check_config.h is included manually, as this can
+     lead to spurious errors. Error if a *adjust*.h header is included
+     manually, as this can lead to silently inconsistent configurations,
+     potentially resulting in buffer overflows.
+     When migrating from Mbed TLS 2.x, if you had a custom config.h that
+     included check_config.h, remove this inclusion from the Mbed TLS 3.x
+     configuration file (renamed to mbedtls_config.h). This change was made
+     in Mbed TLS 3.0, but was not announced in a changelog entry at the time.
diff --git a/include/mbedtls/build_info.h b/include/mbedtls/build_info.h
index eab167f38..cf38f9098 100644
--- a/include/mbedtls/build_info.h
+++ b/include/mbedtls/build_info.h
@@ -101,6 +101,13 @@
 #define inline __inline
 #endif
 
+#if defined(MBEDTLS_CONFIG_FILES_READ)
+#error "Something went wrong: MBEDTLS_CONFIG_FILES_READ defined before reading the config files!"
+#endif
+#if defined(MBEDTLS_CONFIG_IS_FINALIZED)
+#error "Something went wrong: MBEDTLS_CONFIG_IS_FINALIZED defined before reading the config files!"
+#endif
+
 /* X.509, TLS and non-PSA crypto configuration */
 #if !defined(MBEDTLS_CONFIG_FILE)
 #include "mbedtls/mbedtls_config.h"
@@ -135,6 +142,12 @@
 #endif
 #endif /* defined(MBEDTLS_PSA_CRYPTO_CONFIG) */
 
+/* Indicate that all configuration files have been read.
+ * It is now time to adjust the configuration (follow through on dependencies,
+ * make PSA and legacy crypto consistent, etc.).
+ */
+#define MBEDTLS_CONFIG_FILES_READ
+
 /* Auto-enable MBEDTLS_CTR_DRBG_USE_128_BIT_KEY if
  * MBEDTLS_AES_ONLY_128_BIT_KEY_LENGTH and MBEDTLS_CTR_DRBG_C defined
  * to ensure a 128-bit key size in CTR_DRBG.
@@ -169,8 +182,13 @@
 
 #include "mbedtls/config_adjust_ssl.h"
 
-/* Make sure all configuration symbols are set before including check_config.h,
- * even the ones that are calculated programmatically. */
+/* Indicate that all configuration symbols are set,
+ * even the ones that are calculated programmatically.
+ * It is now safe to query the configuration (to check it, to size buffers,
+ * etc.).
+ */
+#define MBEDTLS_CONFIG_IS_FINALIZED
+
 #include "mbedtls/check_config.h"
 
 #endif /* MBEDTLS_BUILD_INFO_H */
diff --git a/include/mbedtls/check_config.h b/include/mbedtls/check_config.h
index b3c038dd2..67a05f83b 100644
--- a/include/mbedtls/check_config.h
+++ b/include/mbedtls/check_config.h
@@ -2,6 +2,13 @@
  * \file check_config.h
  *
  * \brief Consistency checks for configuration options
+ *
+ * This is an internal header. Do not include it directly.
+ *
+ * This header is included automatically by all public Mbed TLS headers
+ * (via mbedtls/build_info.h). Do not include it directly in a configuration
+ * file such as mbedtls/mbedtls_config.h or #MBEDTLS_USER_CONFIG_FILE!
+ * It would run at the wrong time due to missing derived symbols.
  */
 /*
  *  Copyright The Mbed TLS Contributors
@@ -12,6 +19,13 @@
 #define MBEDTLS_CHECK_CONFIG_H
 
 /* *INDENT-OFF* */
+
+#if !defined(MBEDTLS_CONFIG_IS_FINALIZED)
+#warning "Do not include mbedtls/check_config.h manually! " \
+         "This may cause spurious errors. " \
+         "It is included automatically at the right point since Mbed TLS 3.0."
+#endif /* !MBEDTLS_CONFIG_IS_FINALIZED */
+
 /*
  * We assume CHAR_BIT is 8 in many places. In practice, this is true on our
  * target platforms, so not an issue, but let's just be extra sure.
diff --git a/include/mbedtls/config_adjust_legacy_crypto.h b/include/mbedtls/config_adjust_legacy_crypto.h
index e477c0796..854116190 100644
--- a/include/mbedtls/config_adjust_legacy_crypto.h
+++ b/include/mbedtls/config_adjust_legacy_crypto.h
@@ -2,6 +2,8 @@
  * \file mbedtls/config_adjust_legacy_crypto.h
  * \brief Adjust legacy configuration configuration
  *
+ * This is an internal header. Do not include it directly.
+ *
  * Automatically enable certain dependencies. Generally, MBEDLTS_xxx
  * configurations need to be explicitly enabled by the user: enabling
  * MBEDTLS_xxx_A but not MBEDTLS_xxx_B when A requires B results in a
@@ -22,6 +24,14 @@
 #ifndef MBEDTLS_CONFIG_ADJUST_LEGACY_CRYPTO_H
 #define MBEDTLS_CONFIG_ADJUST_LEGACY_CRYPTO_H
 
+#if !defined(MBEDTLS_CONFIG_FILES_READ)
+#error "Do not include mbedtls/config_adjust_*.h manually! This can lead to problems, " \
+    "up to and including runtime errors such as buffer overflows. " \
+    "If you're trying to fix a complaint from check_config.h, just remove " \
+    "it from your configuration file: since Mbed TLS 3.0, it is included " \
+    "automatically at the right point."
+#endif /* */
+
 /* Ideally, we'd set those as defaults in mbedtls_config.h, but
  * putting an #ifdef _WIN32 in mbedtls_config.h would confuse config.py.
  *
diff --git a/include/mbedtls/config_adjust_legacy_from_psa.h b/include/mbedtls/config_adjust_legacy_from_psa.h
index 0e4759de7..04bdae61b 100644
--- a/include/mbedtls/config_adjust_legacy_from_psa.h
+++ b/include/mbedtls/config_adjust_legacy_from_psa.h
@@ -2,6 +2,8 @@
  * \file mbedtls/config_adjust_legacy_from_psa.h
  * \brief Adjust PSA configuration: activate legacy implementations
  *
+ * This is an internal header. Do not include it directly.
+ *
  * When MBEDTLS_PSA_CRYPTO_CONFIG is enabled, activate legacy implementations
  * of cryptographic mechanisms as needed to fulfill the needs of the PSA
  * configuration. Generally speaking, we activate a legacy mechanism if
@@ -16,6 +18,14 @@
 #ifndef MBEDTLS_CONFIG_ADJUST_LEGACY_FROM_PSA_H
 #define MBEDTLS_CONFIG_ADJUST_LEGACY_FROM_PSA_H
 
+#if !defined(MBEDTLS_CONFIG_FILES_READ)
+#error "Do not include mbedtls/config_adjust_*.h manually! This can lead to problems, " \
+    "up to and including runtime errors such as buffer overflows. " \
+    "If you're trying to fix a complaint from check_config.h, just remove " \
+    "it from your configuration file: since Mbed TLS 3.0, it is included " \
+    "automatically at the right point."
+#endif /* */
+
 /* Define appropriate ACCEL macros for the p256-m driver.
  * In the future, those should be generated from the drivers JSON description.
  */
diff --git a/include/mbedtls/config_adjust_psa_from_legacy.h b/include/mbedtls/config_adjust_psa_from_legacy.h
index 345661594..14ca14696 100644
--- a/include/mbedtls/config_adjust_psa_from_legacy.h
+++ b/include/mbedtls/config_adjust_psa_from_legacy.h
@@ -2,6 +2,8 @@
  * \file mbedtls/config_adjust_psa_from_legacy.h
  * \brief Adjust PSA configuration: construct PSA configuration from legacy
  *
+ * This is an internal header. Do not include it directly.
+ *
  * When MBEDTLS_PSA_CRYPTO_CONFIG is disabled, we automatically enable
  * cryptographic mechanisms through the PSA interface when the corresponding
  * legacy mechanism is enabled. In many cases, this just enables the PSA
@@ -18,6 +20,14 @@
 #ifndef MBEDTLS_CONFIG_ADJUST_PSA_FROM_LEGACY_H
 #define MBEDTLS_CONFIG_ADJUST_PSA_FROM_LEGACY_H
 
+#if !defined(MBEDTLS_CONFIG_FILES_READ)
+#error "Do not include mbedtls/config_adjust_*.h manually! This can lead to problems, " \
+    "up to and including runtime errors such as buffer overflows. " \
+    "If you're trying to fix a complaint from check_config.h, just remove " \
+    "it from your configuration file: since Mbed TLS 3.0, it is included " \
+    "automatically at the right point."
+#endif /* */
+
 /*
  * Ensure PSA_WANT_* defines are setup properly if MBEDTLS_PSA_CRYPTO_CONFIG
  * is not defined
diff --git a/include/mbedtls/config_adjust_psa_superset_legacy.h b/include/mbedtls/config_adjust_psa_superset_legacy.h
index 3a55c3f6e..ef65cce0d 100644
--- a/include/mbedtls/config_adjust_psa_superset_legacy.h
+++ b/include/mbedtls/config_adjust_psa_superset_legacy.h
@@ -2,6 +2,8 @@
  * \file mbedtls/config_adjust_psa_superset_legacy.h
  * \brief Adjust PSA configuration: automatic enablement from legacy
  *
+ * This is an internal header. Do not include it directly.
+ *
  * To simplify some edge cases, we automatically enable certain cryptographic
  * mechanisms in the PSA API if they are enabled in the legacy API. The general
  * idea is that if legacy module M uses mechanism A internally, and A has
@@ -17,6 +19,14 @@
 #ifndef MBEDTLS_CONFIG_ADJUST_PSA_SUPERSET_LEGACY_H
 #define MBEDTLS_CONFIG_ADJUST_PSA_SUPERSET_LEGACY_H
 
+#if !defined(MBEDTLS_CONFIG_FILES_READ)
+#error "Do not include mbedtls/config_adjust_*.h manually! This can lead to problems, " \
+    "up to and including runtime errors such as buffer overflows. " \
+    "If you're trying to fix a complaint from check_config.h, just remove " \
+    "it from your configuration file: since Mbed TLS 3.0, it is included " \
+    "automatically at the right point."
+#endif /* */
+
 /****************************************************************/
 /* Hashes that are built in are also enabled in PSA.
  * This simplifies dependency declarations especially
diff --git a/include/mbedtls/config_adjust_ssl.h b/include/mbedtls/config_adjust_ssl.h
index 39c7b3b11..309524a06 100644
--- a/include/mbedtls/config_adjust_ssl.h
+++ b/include/mbedtls/config_adjust_ssl.h
@@ -2,6 +2,8 @@
  * \file mbedtls/config_adjust_ssl.h
  * \brief Adjust TLS configuration
  *
+ * This is an internal header. Do not include it directly.
+ *
  * Automatically enable certain dependencies. Generally, MBEDLTS_xxx
  * configurations need to be explicitly enabled by the user: enabling
  * MBEDTLS_xxx_A but not MBEDTLS_xxx_B when A requires B results in a
@@ -22,6 +24,14 @@
 #ifndef MBEDTLS_CONFIG_ADJUST_SSL_H
 #define MBEDTLS_CONFIG_ADJUST_SSL_H
 
+#if !defined(MBEDTLS_CONFIG_FILES_READ)
+#error "Do not include mbedtls/config_adjust_*.h manually! This can lead to problems, " \
+    "up to and including runtime errors such as buffer overflows. " \
+    "If you're trying to fix a complaint from check_config.h, just remove " \
+    "it from your configuration file: since Mbed TLS 3.0, it is included " \
+    "automatically at the right point."
+#endif /* */
+
 /* The following blocks make it easier to disable all of TLS,
  * or of TLS 1.2 or 1.3 or DTLS, without having to manually disable all
  * key exchanges, options and extensions related to them. */
diff --git a/include/mbedtls/config_adjust_x509.h b/include/mbedtls/config_adjust_x509.h
index 346c8ae6d..c063251b0 100644
--- a/include/mbedtls/config_adjust_x509.h
+++ b/include/mbedtls/config_adjust_x509.h
@@ -2,6 +2,8 @@
  * \file mbedtls/config_adjust_x509.h
  * \brief Adjust X.509 configuration
  *
+ * This is an internal header. Do not include it directly.
+ *
  * Automatically enable certain dependencies. Generally, MBEDLTS_xxx
  * configurations need to be explicitly enabled by the user: enabling
  * MBEDTLS_xxx_A but not MBEDTLS_xxx_B when A requires B results in a
@@ -22,4 +24,12 @@
 #ifndef MBEDTLS_CONFIG_ADJUST_X509_H
 #define MBEDTLS_CONFIG_ADJUST_X509_H
 
+#if !defined(MBEDTLS_CONFIG_FILES_READ)
+#error "Do not include mbedtls/config_adjust_*.h manually! This can lead to problems, " \
+    "up to and including runtime errors such as buffer overflows. " \
+    "If you're trying to fix a complaint from check_config.h, just remove " \
+    "it from your configuration file: since Mbed TLS 3.0, it is included " \
+    "automatically at the right point."
+#endif /* */
+
 #endif /* MBEDTLS_CONFIG_ADJUST_X509_H */
diff --git a/include/psa/crypto_adjust_auto_enabled.h b/include/psa/crypto_adjust_auto_enabled.h
index 63fb29e85..3a2af1518 100644
--- a/include/psa/crypto_adjust_auto_enabled.h
+++ b/include/psa/crypto_adjust_auto_enabled.h
@@ -2,6 +2,8 @@
  * \file psa/crypto_adjust_auto_enabled.h
  * \brief Adjust PSA configuration: enable always-on features
  *
+ * This is an internal header. Do not include it directly.
+ *
  * Always enable certain features which require a negligible amount of code
  * to implement, to avoid some edge cases in the configuration combinatorics.
  */
@@ -13,6 +15,14 @@
 #ifndef PSA_CRYPTO_ADJUST_AUTO_ENABLED_H
 #define PSA_CRYPTO_ADJUST_AUTO_ENABLED_H
 
+#if !defined(MBEDTLS_CONFIG_FILES_READ)
+#error "Do not include psa/crypto_adjust_*.h manually! This can lead to problems, " \
+    "up to and including runtime errors such as buffer overflows. " \
+    "If you're trying to fix a complaint from check_config.h, just remove " \
+    "it from your configuration file: since Mbed TLS 3.0, it is included " \
+    "automatically at the right point."
+#endif /* */
+
 #define PSA_WANT_KEY_TYPE_DERIVE 1
 #define PSA_WANT_KEY_TYPE_PASSWORD 1
 #define PSA_WANT_KEY_TYPE_PASSWORD_HASH 1
diff --git a/include/psa/crypto_adjust_config_dependencies.h b/include/psa/crypto_adjust_config_dependencies.h
index 5a22205bf..92e9c4de2 100644
--- a/include/psa/crypto_adjust_config_dependencies.h
+++ b/include/psa/crypto_adjust_config_dependencies.h
@@ -18,6 +18,14 @@
 #ifndef PSA_CRYPTO_ADJUST_CONFIG_DEPENDENCIES_H
 #define PSA_CRYPTO_ADJUST_CONFIG_DEPENDENCIES_H
 
+#if !defined(MBEDTLS_CONFIG_FILES_READ)
+#error "Do not include psa/crypto_adjust_*.h manually! This can lead to problems, " \
+    "up to and including runtime errors such as buffer overflows. " \
+    "If you're trying to fix a complaint from check_config.h, just remove " \
+    "it from your configuration file: since Mbed TLS 3.0, it is included " \
+    "automatically at the right point."
+#endif /* */
+
 #if (defined(PSA_WANT_ALG_TLS12_PRF) && \
     !defined(MBEDTLS_PSA_ACCEL_ALG_TLS12_PRF)) || \
     (defined(PSA_WANT_ALG_TLS12_PSK_TO_MS) && \
diff --git a/include/psa/crypto_adjust_config_key_pair_types.h b/include/psa/crypto_adjust_config_key_pair_types.h
index 63afc0e40..cec39e01c 100644
--- a/include/psa/crypto_adjust_config_key_pair_types.h
+++ b/include/psa/crypto_adjust_config_key_pair_types.h
@@ -2,6 +2,8 @@
  * \file psa/crypto_adjust_config_key_pair_types.h
  * \brief Adjust PSA configuration for key pair types.
  *
+ * This is an internal header. Do not include it directly.
+ *
  * See docs/proposed/psa-conditional-inclusion-c.md.
  * - Support non-basic operations in a keypair type implicitly enables basic
  *   support for that keypair type.
@@ -19,6 +21,14 @@
 #ifndef PSA_CRYPTO_ADJUST_KEYPAIR_TYPES_H
 #define PSA_CRYPTO_ADJUST_KEYPAIR_TYPES_H
 
+#if !defined(MBEDTLS_CONFIG_FILES_READ)
+#error "Do not include psa/crypto_adjust_*.h manually! This can lead to problems, " \
+    "up to and including runtime errors such as buffer overflows. " \
+    "If you're trying to fix a complaint from check_config.h, just remove " \
+    "it from your configuration file: since Mbed TLS 3.0, it is included " \
+    "automatically at the right point."
+#endif /* */
+
 /*****************************************************************
  * ANYTHING -> BASIC
  ****************************************************************/
diff --git a/include/psa/crypto_adjust_config_synonyms.h b/include/psa/crypto_adjust_config_synonyms.h
index 332b622c9..54b116f43 100644
--- a/include/psa/crypto_adjust_config_synonyms.h
+++ b/include/psa/crypto_adjust_config_synonyms.h
@@ -2,6 +2,8 @@
  * \file psa/crypto_adjust_config_synonyms.h
  * \brief Adjust PSA configuration: enable quasi-synonyms
  *
+ * This is an internal header. Do not include it directly.
+ *
  * When two features require almost the same code, we automatically enable
  * both when either one is requested, to reduce the combinatorics of
  * possible configurations.
@@ -14,6 +16,14 @@
 #ifndef PSA_CRYPTO_ADJUST_CONFIG_SYNONYMS_H
 #define PSA_CRYPTO_ADJUST_CONFIG_SYNONYMS_H
 
+#if !defined(MBEDTLS_CONFIG_FILES_READ)
+#error "Do not include psa/crypto_adjust_*.h manually! This can lead to problems, " \
+    "up to and including runtime errors such as buffer overflows. " \
+    "If you're trying to fix a complaint from check_config.h, just remove " \
+    "it from your configuration file: since Mbed TLS 3.0, it is included " \
+    "automatically at the right point."
+#endif /* */
+
 /****************************************************************/
 /* De facto synonyms */
 /****************************************************************/