diff --git a/packages/auto-instrumentations-node/src/utils.ts b/packages/auto-instrumentations-node/src/utils.ts
index eea8d06869..8dbe604926 100644
--- a/packages/auto-instrumentations-node/src/utils.ts
+++ b/packages/auto-instrumentations-node/src/utils.ts
@@ -166,15 +166,35 @@ export function getNodeAutoInstrumentations(
     // Defaults are defined by the instrumentation itself
     const userConfig: any = inputConfigs[name] ?? {};
 
-    if (
-      userConfig.enabled === false ||
-      !enabledInstrumentationsFromEnv.includes(name) ||
-      disabledInstrumentationsFromEnv.includes(name)
-    ) {
-      diag.debug(`Disabling instrumentation for ${name}`);
+    // Configuration priority: Environment variables > programmatic config
+    // If both OTEL_NODE_ENABLED_INSTRUMENTATIONS and OTEL_NODE_DISABLED_INSTRUMENTATIONS are set, ENABLED is applied first, then DISABLED is applied to that list.
+    // If the same instrumentation is in both lists, it will be disabled.
+    // When env vars are unset, allow programmatic config to override default exclusions
+
+    if (disabledInstrumentationsFromEnv.includes(name)) {
+      diag.debug(`Disabling instrumentation for ${name} - disabled by env var`);
       continue;
     }
 
+    const isEnabledEnvSet = !!process.env.OTEL_NODE_ENABLED_INSTRUMENTATIONS;
+    if (isEnabledEnvSet) {
+      if (!enabledInstrumentationsFromEnv.includes(name)) {
+        diag.debug(`Disabling instrumentation for ${name} - not in enabled env var list`);
+        continue;
+      }
+    } else {
+      if (userConfig.enabled === false) {
+        diag.debug(`Disabling instrumentation for ${name} - disabled by user config`);
+        continue;
+      }
+
+      const isDefaultExcluded = defaultExcludedInstrumentations.includes(name);
+      if (isDefaultExcluded && userConfig.enabled !== true) {
+        diag.debug(`Disabling instrumentation for ${name} - excluded by default and not explicitly enabled`);
+        continue;
+      }
+    }
+
     try {
       diag.debug(`Loading instrumentation for ${name}`);
       instrumentations.push(new Instance(userConfig));
diff --git a/packages/auto-instrumentations-node/test/utils.test.ts b/packages/auto-instrumentations-node/test/utils.test.ts
index 1241ca6cce..d65678273c 100644
--- a/packages/auto-instrumentations-node/test/utils.test.ts
+++ b/packages/auto-instrumentations-node/test/utils.test.ts
@@ -172,6 +172,76 @@ describe('utils', () => {
 
       spy.restore();
     });
+
+    it('should enable fs instrumentation when explicitly enabled and OTEL_NODE_ENABLED_INSTRUMENTATIONS is not set', () => {
+      const instrumentations = getNodeAutoInstrumentations({
+        '@opentelemetry/instrumentation-fs': {
+          enabled: true,
+        },
+      });
+      const fsInstrumentation = instrumentations.find(
+        instr =>
+          instr.instrumentationName === '@opentelemetry/instrumentation-fs'
+      );
+      assert.notStrictEqual(
+        fsInstrumentation,
+        undefined,
+        'fs instrumentation should be included when explicitly enabled in config and env var is not set'
+      );
+    });
+
+    it('should respect OTEL_NODE_ENABLED_INSTRUMENTATIONS - env var overrides user config', () => {
+      process.env.OTEL_NODE_ENABLED_INSTRUMENTATIONS = 'fs,http';
+      try {
+        const instrumentations = getNodeAutoInstrumentations({
+          '@opentelemetry/instrumentation-fs': {
+            enabled: false, // User tries to disable but env var overrides
+          },
+          '@opentelemetry/instrumentation-express': {
+            enabled: true, // User tries to enable but not in env var list
+          },
+        });
+        
+        const fsInstrumentation = instrumentations.find(
+          instr => instr.instrumentationName === '@opentelemetry/instrumentation-fs'
+        );
+        const httpInstrumentation = instrumentations.find(
+          instr => instr.instrumentationName === '@opentelemetry/instrumentation-http'
+        );
+        const expressInstrumentation = instrumentations.find(
+          instr => instr.instrumentationName === '@opentelemetry/instrumentation-express'
+        );
+        
+        assert.notStrictEqual(fsInstrumentation, undefined, 'fs should be enabled by env var despite user config');
+        assert.notStrictEqual(httpInstrumentation, undefined, 'http should be enabled by env var');
+        assert.strictEqual(expressInstrumentation, undefined, 'express should be disabled - not in env var list');
+      } finally {
+        delete process.env.OTEL_NODE_ENABLED_INSTRUMENTATIONS;
+      }
+    });
+
+    it('should respect OTEL_NODE_DISABLED_INSTRUMENTATIONS with absolute priority', () => {
+      process.env.OTEL_NODE_DISABLED_INSTRUMENTATIONS = 'http';
+      try {
+        const instrumentations = getNodeAutoInstrumentations({
+          '@opentelemetry/instrumentation-http': {
+            enabled: true, // User tries to enable but env var disables
+          },
+        });
+        const httpInstrumentation = instrumentations.find(
+          instr =>
+            instr.instrumentationName === '@opentelemetry/instrumentation-http'
+        );
+        
+        assert.strictEqual(
+          httpInstrumentation,
+          undefined,
+          'http instrumentation should be disabled by OTEL_NODE_DISABLED_INSTRUMENTATIONS even when user enables it'
+        );
+      } finally {
+        delete process.env.OTEL_NODE_DISABLED_INSTRUMENTATIONS;
+      }
+    });
   });
 
   describe('getResourceDetectorsFromEnv', () => {