diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index ba7a345b1f..8917590929 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -65,6 +65,15 @@ jobs:
           - php: '8.4'
             skip_tests: true
 
+          # Run a couple of builds with custom extensions to allow for testing ini handling within PHPCS.
+          # Ref: https://github.com/PHPCSStandards/PHP_CodeSniffer/issues/416
+          - php: '7.3'
+            os: 'ubuntu-latest'
+            extensions: ':mysqli' # Run with mysqli disabled.
+          - php: '8.2'
+            os: 'ubuntu-latest'
+            extensions: ':mysqli' # Run with mysqli disabled.
+
           # The default libxml library on Ubuntu images is a little out of date.
           # To safeguard support for the latest libxml we need to update the library on the fly.
           # This only needs to be tested with one PHP version for each libxml minor to verify support.
@@ -183,6 +192,7 @@ jobs:
         with:
           php-version: ${{ matrix.php }}
           ini-values: ${{ steps.set_ini.outputs.PHP_INI }}
+          extensions: ${{ matrix.extensions }}
           coverage: none
           tools: cs2pr
 
@@ -269,10 +279,12 @@ jobs:
         custom_ini: [false]
 
         include:
-          # Also run one coverage build with custom ini settings.
+          # Also run one coverage build with custom ini settings for testing the DisallowShortOpenTag sniff.
+          # Also run with a disabled extension for testing the handling of unsettable ini settings by PHPCS.
           - php: '8.1'
             os: 'ubuntu-latest'
             custom_ini: true
+            extensions: ':mysqli' # Run with mysqli disabled.
 
     # yamllint disable-line rule:line-length
     name: "Coverage: ${{ matrix.php }} ${{ matrix.custom_ini && ' with custom ini settings' || '' }} (${{ matrix.os == 'ubuntu-latest' && 'Linux' || 'Win'  }})"
@@ -297,6 +309,7 @@ jobs:
         with:
           php-version: ${{ matrix.php }}
           ini-values: error_reporting=-1, display_errors=On${{ steps.set_ini.outputs.PHP_INI }}
+          extensions: ${{ matrix.extensions }}
           coverage: xdebug
 
       # Install dependencies and handle caching in one go.
diff --git a/src/Config.php b/src/Config.php
index 1c8d8dbdd1..c0494dbabc 100644
--- a/src/Config.php
+++ b/src/Config.php
@@ -739,10 +739,23 @@ public function processShortArgument($arg, $pos)
         case 'd' :
             $ini = explode('=', $this->cliArgs[($pos + 1)]);
             $this->cliArgs[($pos + 1)] = '';
-            if (isset($ini[1]) === true) {
-                ini_set($ini[0], $ini[1]);
-            } else {
-                ini_set($ini[0], true);
+            if (isset($ini[1]) === false) {
+                // Set to true.
+                $ini[1] = '1';
+            }
+
+            $current = ini_get($ini[0]);
+            if ($current === false) {
+                // Ini setting which doesn't exist, or is from an unavailable extension.
+                // Silently ignore it.
+                break;
+            }
+
+            $changed = ini_set($ini[0], $ini[1]);
+            if ($changed === false && ini_get($ini[0]) !== $ini[1]) {
+                $error  = sprintf('ERROR: Ini option "%s" cannot be changed at runtime.', $ini[0]).PHP_EOL;
+                $error .= $this->printShortUsage(true);
+                throw new DeepExitException($error, 3);
             }
             break;
         case 'n' :
diff --git a/tests/Core/Config/IniSetTest.php b/tests/Core/Config/IniSetTest.php
new file mode 100644
index 0000000000..d9977f6d3a
--- /dev/null
+++ b/tests/Core/Config/IniSetTest.php
@@ -0,0 +1,328 @@
+<?php
+/**
+ * Tests for overriding the value of a PHP ini setting using CLI arguments.
+ *
+ * @copyright 2025 PHPCSStandards Contributors
+ * @license   https://github.com/PHPCSStandards/PHP_CodeSniffer/blob/master/licence.txt BSD Licence
+ */
+
+namespace PHP_CodeSniffer\Tests\Core\Config;
+
+use PHP_CodeSniffer\Exceptions\DeepExitException;
+use PHP_CodeSniffer\Tests\ConfigDouble;
+use PHPUnit\Framework\TestCase;
+
+/**
+ * Tests for overriding the value of a PHP ini setting using CLI arguments.
+ *
+ * @covers \PHP_CodeSniffer\Config::processShortArgument
+ */
+final class IniSetTest extends TestCase
+{
+
+    /**
+     * The name of the current ini setting under test.
+     *
+     * @var string
+     */
+    private $currentOption;
+
+    /**
+     * Store the original value of the ini setting under test, so the system can be restored to its
+     * original state in the tearDown() method.
+     *
+     * @var string|false
+     */
+    private $originalValue;
+
+
+    /**
+     * Reset the ini value which was potentially changed via the test.
+     *
+     * @return void
+     */
+    protected function tearDown(): void
+    {
+        if (is_string($this->originalValue) === true) {
+            @ini_set($this->currentOption, $this->originalValue);
+        }
+
+    }//end tearDown()
+
+
+    /**
+     * Verify that when an ini option is passed on the command-line and the value is the current value of the option
+     * and can be set at runtime, PHPCS does not throw an exception.
+     *
+     * @return void
+     */
+    public function testIniValueHandlingWhenValueIsAlreadyCorrect()
+    {
+        $this->currentOption = 'precision';
+        $this->originalValue = ini_get($this->currentOption);
+
+        $this->assertNotFalse($this->originalValue, "Test is broken: the {$this->currentOption} ini directive does not exist");
+
+        new ConfigDouble(['-d', "{$this->currentOption}={$this->originalValue}"]);
+
+        $this->assertSame($this->originalValue, ini_get($this->currentOption));
+
+    }//end testIniValueHandlingWhenValueIsAlreadyCorrect()
+
+
+    /**
+     * Verify that when an ini option is passed on the command-line without a value and can be set at runtime, PHPCS sets it correctly.
+     *
+     * @requires extension mbstring
+     *
+     * @return void
+     */
+    public function testIniValueIsUpdatedToTrueWhenNoValuePassed()
+    {
+        $this->currentOption = 'precision';
+        // Set the expectation as the string equivalent to "true" as ini_get() will return a string value.
+        $expected = '1';
+
+        $this->originalValue = ini_get($this->currentOption);
+
+        if ($this->originalValue === $expected) {
+            $this->markTestSkipped(
+                'Skipping as original ini value on the system on which the test is run, is the same as the intended "new" value.'
+            );
+        }
+
+        $this->assertNotFalse($this->originalValue, "Test is broken: the {$this->currentOption} ini directive does not exist");
+
+        new ConfigDouble(['-d', $this->currentOption]);
+
+        $this->assertSame($expected, ini_get($this->currentOption));
+
+    }//end testIniValueIsUpdatedToTrueWhenNoValuePassed()
+
+
+    /**
+     * Test that when an ini value for a Core directive is passed on the command-line and can be set at runtime,
+     * PHPCS sets it correctly.
+     *
+     * @param string $option           The name of the ini option.
+     * @param string $newValue         The value to set the ini option to.
+     * @param string $alternativeValue Alternative value if the newValue would happen to coincide with the original value.
+     *
+     * @dataProvider dataIniValueIsUpdated
+     *
+     * @return void
+     */
+    public function testIniValueIsUpdated($option, $newValue, $alternativeValue)
+    {
+        $this->currentOption = $option;
+        $this->originalValue = ini_get($option);
+
+        if ($this->originalValue === $newValue) {
+            $newValue = $alternativeValue;
+        }
+
+        $this->assertNotFalse($this->originalValue, "Test is broken: the $option ini directive does not exist");
+
+        new ConfigDouble(['-d', "$option=$newValue"]);
+
+        $this->assertSame($newValue, ini_get($option));
+
+    }//end testIniValueIsUpdated()
+
+
+    /**
+     * Data provider.
+     *
+     * @return array<string, array<string, string>>
+     */
+    public static function dataIniValueIsUpdated()
+    {
+        return [
+            // Core directive, default value is 14.
+            'INI_ALL option: precision' => [
+                'option'           => 'precision',
+                'newValue'         => '10',
+                'alternativeValue' => '20',
+            ],
+        ];
+
+    }//end dataIniValueIsUpdated()
+
+
+    /**
+     * Test that when an INI_ALL value for an optional extension is passed on the command-line and can be set at runtime,
+     * PHPCS sets it correctly.
+     *
+     * This is tested in a separate method as the BCMath extension may not be available (which would cause the test to fail).
+     *
+     * @requires extension bcmath
+     *
+     * @return void
+     */
+    public function testIniValueIsUpdatedWhenOptionalBcmathExtensionIsAvailable()
+    {
+        // Default value for the bcmath.scale ini setting is 0.
+        $this->currentOption = 'bcmath.scale';
+        $newValue            = '10';
+
+        $this->originalValue = ini_get($this->currentOption);
+        if ($this->originalValue === $newValue) {
+            $newValue = '20';
+        }
+
+        $this->assertNotFalse($this->originalValue, "Test is broken: the {$this->currentOption} ini directive does not exist");
+
+        new ConfigDouble(['-d', "{$this->currentOption}=$newValue"]);
+
+        $this->assertSame($newValue, ini_get($this->currentOption));
+
+    }//end testIniValueIsUpdatedWhenOptionalBcmathExtensionIsAvailable()
+
+
+    /**
+     * Test that when an ini value is passed on the command-line and can be set at runtime, PHPCS sets it correctly.
+     *
+     * There are only two `INI_USER` options in PHP. The first `tidy.clean_output` cannot be used for this test
+     * as PHPUnit will send headers before this test runs.
+     * So `sqlite3.defensive` is the only option we can test with, but this option was an INI_SYSTEM setting
+     * prior to PHP 8.2, so we can only test it on PHP 8.2 and higher.
+     *
+     * It's also unfortunate that it is a boolean option, which makes distinguising "set to false" and
+     * "not set" difficult.
+     *
+     * @requires PHP 8.2
+     * @requires extension sqlite3
+     *
+     * @return void
+     */
+    public function testIniValueIsUpdatedWhenOptionalSqllite3ExtensionIsAvailable()
+    {
+        // Default value for the sqlite3.defensive ini setting is 1.
+        $this->currentOption = 'sqlite3.defensive';
+        $newValue            = '0';
+
+        $this->originalValue = ini_get($this->currentOption);
+        if ($this->originalValue === $newValue) {
+            $newValue = '1';
+        }
+
+        $this->assertNotFalse($this->originalValue, "Test is broken: the {$this->currentOption} ini directive does not exist");
+
+        new ConfigDouble(['-d', "{$this->currentOption}=$newValue"]);
+
+        $this->assertSame($newValue, ini_get($this->currentOption));
+
+    }//end testIniValueIsUpdatedWhenOptionalSqllite3ExtensionIsAvailable()
+
+
+    /**
+     * Test that when an ini value is for a disabled extension, PHPCS will silently ignore the ini setting.
+     *
+     * @return void
+     */
+    public function testIniValueIsSilentlyIgnoredWhenOptionalExtensionIsNotAvailable()
+    {
+        if (extension_loaded('mysqli') === true) {
+            $this->markTestSkipped(
+                'Skipping as this test needs the MySqli extension to *not* be available.'
+            );
+        }
+
+        $this->currentOption = 'mysqli.default_port';
+        $newValue            = '1234';
+
+        $this->originalValue = ini_get($this->currentOption);
+        $this->assertFalse($this->originalValue, "Test is broken: the {$this->currentOption} ini directive exists");
+
+        new ConfigDouble(['-d', "{$this->currentOption}=$newValue"]);
+
+        $this->assertFalse(ini_get($this->currentOption), 'This should be impossible: an option for a disabled extension cannot be set');
+
+    }//end testIniValueIsSilentlyIgnoredWhenOptionalExtensionIsNotAvailable()
+
+
+    /**
+     * Test that when an ini value is not known to PHP, PHPCS will silently ignore the ini setting.
+     *
+     * @return void
+     */
+    public function testIniValueIsSilentlyIgnoredForUnknownIniName()
+    {
+        $this->currentOption = 'some.ini_which_doesnt_exist';
+        $newValue            = '1234';
+
+        $this->originalValue = ini_get($this->currentOption);
+        $this->assertFalse($this->originalValue, "Test is broken: the {$this->currentOption} ini directive exists");
+
+        new ConfigDouble(['-d', "{$this->currentOption}=$newValue"]);
+
+        $this->assertFalse(ini_get($this->currentOption), 'This should be impossible: an option which isn\'t known to PHP cannot be set');
+
+    }//end testIniValueIsSilentlyIgnoredForUnknownIniName()
+
+
+    /**
+     * Test that when an ini value is passed on the command-line and can NOT be set at runtime, PHPCS reports this.
+     *
+     * @param string $option           The name of the ini option.
+     * @param string $newValue         The value to set the ini option to.
+     * @param string $alternativeValue Alternative value in case the ini option is currently set to the $newValue.
+     *
+     * @dataProvider dataIniValueCannotBeUpdatedAtRuntime
+     *
+     * @return void
+     */
+    public function testIniValueCannotBeUpdatedAtRuntime($option, $newValue, $alternativeValue='')
+    {
+        $this->expectException(DeepExitException::class);
+        $this->expectExceptionMessage("ERROR: Ini option \"$option\" cannot be changed at runtime.");
+
+        $this->currentOption = $option;
+        $this->originalValue = ini_get($option);
+        $this->assertNotFalse($this->originalValue, "Test is broken: the $option ini directive does not exist");
+
+        if ($this->originalValue === $newValue) {
+            $newValue = $alternativeValue;
+        }
+
+        new ConfigDouble(['-d', "$option=$newValue"]);
+
+    }//end testIniValueCannotBeUpdatedAtRuntime()
+
+
+    /**
+     * Data provider.
+     *
+     * @return array<string, array<string, string>>
+     */
+    public static function dataIniValueCannotBeUpdatedAtRuntime()
+    {
+        return [
+            // Using Core directives available PHP cross-version to prevent the tests failing
+            // on an unavailable directive or due to an extension not being available.
+            'php.ini only option: disable_classes'     => [
+                'option'           => 'disable_classes',
+                'newValue'         => 'DateTime,DOMComment',
+                'alternativeValue' => 'DOMComment,DateTime',
+            ],
+            'INI_PERDIR option: short_open_tag (bool)' => [
+                'option'           => 'short_open_tag',
+                'newValue'         => '1',
+                'alternativeValue' => '0',
+            ],
+            'INI_PERDIR option: max_input_vars (int)'  => [
+                'option'           => 'max_input_vars',
+                'newValue'         => '345',
+                'alternativeValue' => '543',
+            ],
+            'INI_SYSTEM option: realpath_cache_ttl'    => [
+                'option'           => 'realpath_cache_ttl',
+                'newValue'         => '150',
+                'alternativeValue' => '300',
+            ],
+        ];
+
+    }//end dataIniValueCannotBeUpdatedAtRuntime()
+
+
+}//end class
diff --git a/tests/Core/Ruleset/IniSetFailIniOnlyTest.xml b/tests/Core/Ruleset/IniSetFailIniOnlyTest.xml
new file mode 100644
index 0000000000..73476fdfb3
--- /dev/null
+++ b/tests/Core/Ruleset/IniSetFailIniOnlyTest.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0"?>
+<ruleset xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" name="IniSetTest" xsi:noNamespaceSchemaLocation="phpcs.xsd">
+    <description>Ruleset to test ini values which can not be changed at runtime will be reported as such when set from the ruleset.</description>
+
+    <ini name="disable_classes" value="DateTime,DOMComment"/>
+
+    <!-- Prevent a "no sniff were registered" error. -->
+    <rule ref="Generic.PHP.BacktickOperator"/>
+</ruleset>
diff --git a/tests/Core/Ruleset/IniSetFailIniPerDirTest.xml b/tests/Core/Ruleset/IniSetFailIniPerDirTest.xml
new file mode 100644
index 0000000000..87b9eecaf9
--- /dev/null
+++ b/tests/Core/Ruleset/IniSetFailIniPerDirTest.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0"?>
+<ruleset xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" name="IniSetTest" xsi:noNamespaceSchemaLocation="phpcs.xsd">
+    <description>Ruleset to test ini values which can not be changed at runtime will be reported as such when set from the ruleset.</description>
+
+    <ini name="short_open_tag" value="1"/>
+
+    <!-- Prevent a "no sniff were registered" error. -->
+    <rule ref="Generic.PHP.BacktickOperator"/>
+</ruleset>
diff --git a/tests/Core/Ruleset/IniSetFailIniSystemTest.xml b/tests/Core/Ruleset/IniSetFailIniSystemTest.xml
new file mode 100644
index 0000000000..292cbf7bf1
--- /dev/null
+++ b/tests/Core/Ruleset/IniSetFailIniSystemTest.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0"?>
+<ruleset xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" name="IniSetTest" xsi:noNamespaceSchemaLocation="phpcs.xsd">
+    <description>Ruleset to test ini values which can not be changed at runtime will be reported as such when set from the ruleset.</description>
+
+    <ini name="realpath_cache_ttl" value="200"/>
+
+    <!-- Prevent a "no sniff were registered" error. -->
+    <rule ref="Generic.PHP.BacktickOperator"/>
+</ruleset>
diff --git a/tests/Core/Ruleset/IniSetSuccessTest.xml b/tests/Core/Ruleset/IniSetSuccessTest.xml
new file mode 100644
index 0000000000..81284e1ea2
--- /dev/null
+++ b/tests/Core/Ruleset/IniSetSuccessTest.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0"?>
+<ruleset xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" name="IniSetTest" xsi:noNamespaceSchemaLocation="phpcs.xsd">
+    <description>Ruleset to test ini values can be changed from the ruleset.</description>
+
+    <ini name="precision" value="10"/>
+
+    <!-- Prevent a "no sniff were registered" error. -->
+    <rule ref="Generic.PHP.BacktickOperator"/>
+</ruleset>
diff --git a/tests/Core/Ruleset/ProcessRulesetIniSetTest.php b/tests/Core/Ruleset/ProcessRulesetIniSetTest.php
new file mode 100644
index 0000000000..5b1b4cb1fa
--- /dev/null
+++ b/tests/Core/Ruleset/ProcessRulesetIniSetTest.php
@@ -0,0 +1,139 @@
+<?php
+/**
+ * Tests for overriding the value of a PHP ini setting by passing a new value via a ruleset.
+ *
+ * @copyright 2025 PHPCSStandards Contributors
+ * @license   https://github.com/PHPCSStandards/PHP_CodeSniffer/blob/master/licence.txt BSD Licence
+ */
+
+namespace PHP_CodeSniffer\Tests\Core\Ruleset;
+
+use PHP_CodeSniffer\Exceptions\DeepExitException;
+use PHP_CodeSniffer\Ruleset;
+use PHP_CodeSniffer\Tests\ConfigDouble;
+use PHPUnit\Framework\TestCase;
+
+/**
+ * Tests handling of attempts to override an (un)changeable PHP ini setting by passing a new value via a ruleset.
+ *
+ * @covers \PHP_CodeSniffer\Ruleset::processRuleset
+ */
+final class ProcessRulesetIniSetTest extends TestCase
+{
+
+    /**
+     * The name of the current ini setting under test.
+     *
+     * @var string
+     */
+    private $currentOption;
+
+    /**
+     * Store the original value of the ini setting under test, so the system can be restored to its
+     * original state in the tearDown() method.
+     *
+     * @var string|false
+     */
+    private $originalValue;
+
+
+    /**
+     * Reset the ini value which was potentially changed via the test.
+     *
+     * @return void
+     */
+    protected function tearDown(): void
+    {
+        if (is_string($this->originalValue) === true) {
+            @ini_set($this->currentOption, $this->originalValue);
+        }
+
+    }//end tearDown()
+
+
+    /**
+     * Test that when an ini value is set in a custom ruleset and can be set at runtime, PHPCS sets it correctly.
+     *
+     * @return void
+     */
+    public function testIniValueIsUpdated()
+    {
+        $this->currentOption = 'precision';
+        $expected            = '10';
+
+        $this->originalValue = ini_get($this->currentOption);
+        $this->assertNotFalse($this->originalValue, "Test is broken: the {$this->currentOption} ini directive does not exist");
+
+        new Ruleset(new ConfigDouble(['.', '--standard='.__DIR__.'/IniSetSuccessTest.xml']));
+
+        $this->assertSame($expected, ini_get($this->currentOption));
+
+    }//end testIniValueIsUpdated()
+
+
+    /**
+     * Test that when an ini value is set in a custom ruleset and can NOT be set at runtime, PHPCS reports this.
+     *
+     * @param string $standard The standard to use for the test.
+     * @param string $option   The name of the ini option.
+     * @param mixed  $expected The value to expect the ini option to be set to if it could have been changed.
+     *
+     * @dataProvider dataIniValueCannotBeUpdatedAtRuntime
+     *
+     * @return void
+     */
+    public function testIniValueCannotBeUpdatedAtRuntime($standard, $option, $expected)
+    {
+        $this->currentOption = $option;
+        $this->originalValue = ini_get($option);
+
+        if ($this->originalValue === $expected) {
+            $this->markTestSkipped(
+                'Skipping as original ini value on the system on which the test is run, is the same as the intended "new" value.'
+            );
+        }
+
+        $this->assertNotFalse($this->originalValue, "Test is broken: the $option ini directive does not exist");
+
+        $this->expectException(DeepExitException::class);
+        $this->expectExceptionMessage("ERROR: Ini option \"$option\" cannot be changed at runtime.");
+
+        new Ruleset(new ConfigDouble(["--standard=$standard"]));
+
+        // Make sure the value didn't get set.
+        $this->assertNotSame($expected, ini_get($option), 'Setting the ini value should not have worked, the test is broken');
+
+    }//end testIniValueCannotBeUpdatedAtRuntime()
+
+
+    /**
+     * Data provider.
+     *
+     * @return array<string, array<string, mixed>>
+     */
+    public static function dataIniValueCannotBeUpdatedAtRuntime()
+    {
+        return [
+            // Using Core directives available PHP cross-version to prevent the tests failing
+            // on an unavailable directive or due to an extension not being available.
+            'php.ini only option: disable_classes'  => [
+                'standard' => __DIR__.'/IniSetFailIniOnlyTest.xml',
+                'option'   => 'disable_classes',
+                'expected' => 'DateTime,DOMComment',
+            ],
+            'INI_PERDIR option: short_open_tag'     => [
+                'standard' => __DIR__.'/IniSetFailIniPerDirTest.xml',
+                'option'   => 'short_open_tag',
+                'expected' => '1',
+            ],
+            'INI_SYSTEM option: realpath_cache_ttl' => [
+                'standard' => __DIR__.'/IniSetFailIniSystemTest.xml',
+                'option'   => 'realpath_cache_ttl',
+                'expected' => '200',
+            ],
+        ];
+
+    }//end dataIniValueCannotBeUpdatedAtRuntime()
+
+
+}//end class