diff --git a/lib/analyze-action-post.js b/lib/analyze-action-post.js
index b7888da1e..bccb69ddd 100644
--- a/lib/analyze-action-post.js
+++ b/lib/analyze-action-post.js
@@ -124950,6 +124950,10 @@ async function getCodeQLForCmd(cmd, checkVersion) {
       } else if (overlayDatabaseMode === "overlay-base" /* OverlayBase */) {
         extraArgs.push("--overlay-base");
       }
+      const baselineFilesOptions = config.enableFileCoverageInformation ? [
+        "--calculate-language-specific-baseline",
+        "--sublanguage-file-coverage"
+      ] : ["--no-calculate-baseline"];
       await runCli(
         cmd,
         [
@@ -124959,12 +124963,11 @@ async function getCodeQLForCmd(cmd, checkVersion) {
           "--db-cluster",
           config.dbLocation,
           `--source-root=${sourceRoot}`,
-          "--calculate-language-specific-baseline",
+          ...baselineFilesOptions,
           "--extractor-include-aliases",
-          "--sublanguage-file-coverage",
           ...extraArgs,
           ...getExtraOptionsFromEnv(["database", "init"], {
-            ignoringOptions: ["--overwrite"]
+            ignoringOptions: ["--overwrite", ...baselineFilesOptions]
           })
         ],
         { stdin: externalRepositoryToken }
diff --git a/lib/analyze-action.js b/lib/analyze-action.js
index ae915d822..fa7fdcb0d 100644
--- a/lib/analyze-action.js
+++ b/lib/analyze-action.js
@@ -93050,6 +93050,10 @@ async function getCodeQLForCmd(cmd, checkVersion) {
       } else if (overlayDatabaseMode === "overlay-base" /* OverlayBase */) {
         extraArgs.push("--overlay-base");
       }
+      const baselineFilesOptions = config.enableFileCoverageInformation ? [
+        "--calculate-language-specific-baseline",
+        "--sublanguage-file-coverage"
+      ] : ["--no-calculate-baseline"];
       await runCli(
         cmd,
         [
@@ -93059,12 +93063,11 @@ async function getCodeQLForCmd(cmd, checkVersion) {
           "--db-cluster",
           config.dbLocation,
           `--source-root=${sourceRoot}`,
-          "--calculate-language-specific-baseline",
+          ...baselineFilesOptions,
           "--extractor-include-aliases",
-          "--sublanguage-file-coverage",
           ...extraArgs,
           ...getExtraOptionsFromEnv(["database", "init"], {
-            ignoringOptions: ["--overwrite"]
+            ignoringOptions: ["--overwrite", ...baselineFilesOptions]
           })
         ],
         { stdin: externalRepositoryToken }
diff --git a/lib/autobuild-action.js b/lib/autobuild-action.js
index 7b8c30a9f..1b46f3e60 100644
--- a/lib/autobuild-action.js
+++ b/lib/autobuild-action.js
@@ -88150,6 +88150,10 @@ async function getCodeQLForCmd(cmd, checkVersion) {
       } else if (overlayDatabaseMode === "overlay-base" /* OverlayBase */) {
         extraArgs.push("--overlay-base");
       }
+      const baselineFilesOptions = config.enableFileCoverageInformation ? [
+        "--calculate-language-specific-baseline",
+        "--sublanguage-file-coverage"
+      ] : ["--no-calculate-baseline"];
       await runCli(
         cmd,
         [
@@ -88159,12 +88163,11 @@ async function getCodeQLForCmd(cmd, checkVersion) {
           "--db-cluster",
           config.dbLocation,
           `--source-root=${sourceRoot}`,
-          "--calculate-language-specific-baseline",
+          ...baselineFilesOptions,
           "--extractor-include-aliases",
-          "--sublanguage-file-coverage",
           ...extraArgs,
           ...getExtraOptionsFromEnv(["database", "init"], {
-            ignoringOptions: ["--overwrite"]
+            ignoringOptions: ["--overwrite", ...baselineFilesOptions]
           })
         ],
         { stdin: externalRepositoryToken }
diff --git a/lib/init-action-post.js b/lib/init-action-post.js
index d255aa707..39937f99e 100644
--- a/lib/init-action-post.js
+++ b/lib/init-action-post.js
@@ -129585,6 +129585,10 @@ async function getCodeQLForCmd(cmd, checkVersion) {
       } else if (overlayDatabaseMode === "overlay-base" /* OverlayBase */) {
         extraArgs.push("--overlay-base");
       }
+      const baselineFilesOptions = config.enableFileCoverageInformation ? [
+        "--calculate-language-specific-baseline",
+        "--sublanguage-file-coverage"
+      ] : ["--no-calculate-baseline"];
       await runCli(
         cmd,
         [
@@ -129594,12 +129598,11 @@ async function getCodeQLForCmd(cmd, checkVersion) {
           "--db-cluster",
           config.dbLocation,
           `--source-root=${sourceRoot}`,
-          "--calculate-language-specific-baseline",
+          ...baselineFilesOptions,
           "--extractor-include-aliases",
-          "--sublanguage-file-coverage",
           ...extraArgs,
           ...getExtraOptionsFromEnv(["database", "init"], {
-            ignoringOptions: ["--overwrite"]
+            ignoringOptions: ["--overwrite", ...baselineFilesOptions]
           })
         ],
         { stdin: externalRepositoryToken }
diff --git a/lib/init-action.js b/lib/init-action.js
index 0832e5bde..f11ff5930 100644
--- a/lib/init-action.js
+++ b/lib/init-action.js
@@ -91400,6 +91400,10 @@ async function getCodeQLForCmd(cmd, checkVersion) {
       } else if (overlayDatabaseMode === "overlay-base" /* OverlayBase */) {
         extraArgs.push("--overlay-base");
       }
+      const baselineFilesOptions = config.enableFileCoverageInformation ? [
+        "--calculate-language-specific-baseline",
+        "--sublanguage-file-coverage"
+      ] : ["--no-calculate-baseline"];
       await runCli(
         cmd,
         [
@@ -91409,12 +91413,11 @@ async function getCodeQLForCmd(cmd, checkVersion) {
           "--db-cluster",
           config.dbLocation,
           `--source-root=${sourceRoot}`,
-          "--calculate-language-specific-baseline",
+          ...baselineFilesOptions,
           "--extractor-include-aliases",
-          "--sublanguage-file-coverage",
           ...extraArgs,
           ...getExtraOptionsFromEnv(["database", "init"], {
-            ignoringOptions: ["--overwrite"]
+            ignoringOptions: ["--overwrite", ...baselineFilesOptions]
           })
         ],
         { stdin: externalRepositoryToken }
diff --git a/lib/resolve-environment-action.js b/lib/resolve-environment-action.js
index 8630b474a..a62917f01 100644
--- a/lib/resolve-environment-action.js
+++ b/lib/resolve-environment-action.js
@@ -87843,6 +87843,10 @@ async function getCodeQLForCmd(cmd, checkVersion) {
       } else if (overlayDatabaseMode === "overlay-base" /* OverlayBase */) {
         extraArgs.push("--overlay-base");
       }
+      const baselineFilesOptions = config.enableFileCoverageInformation ? [
+        "--calculate-language-specific-baseline",
+        "--sublanguage-file-coverage"
+      ] : ["--no-calculate-baseline"];
       await runCli(
         cmd,
         [
@@ -87852,12 +87856,11 @@ async function getCodeQLForCmd(cmd, checkVersion) {
           "--db-cluster",
           config.dbLocation,
           `--source-root=${sourceRoot}`,
-          "--calculate-language-specific-baseline",
+          ...baselineFilesOptions,
           "--extractor-include-aliases",
-          "--sublanguage-file-coverage",
           ...extraArgs,
           ...getExtraOptionsFromEnv(["database", "init"], {
-            ignoringOptions: ["--overwrite"]
+            ignoringOptions: ["--overwrite", ...baselineFilesOptions]
           })
         ],
         { stdin: externalRepositoryToken }
diff --git a/lib/setup-codeql-action.js b/lib/setup-codeql-action.js
index 308ef03c6..0a480cea1 100644
--- a/lib/setup-codeql-action.js
+++ b/lib/setup-codeql-action.js
@@ -89152,6 +89152,10 @@ async function getCodeQLForCmd(cmd, checkVersion) {
       } else if (overlayDatabaseMode === "overlay-base" /* OverlayBase */) {
         extraArgs.push("--overlay-base");
       }
+      const baselineFilesOptions = config.enableFileCoverageInformation ? [
+        "--calculate-language-specific-baseline",
+        "--sublanguage-file-coverage"
+      ] : ["--no-calculate-baseline"];
       await runCli(
         cmd,
         [
@@ -89161,12 +89165,11 @@ async function getCodeQLForCmd(cmd, checkVersion) {
           "--db-cluster",
           config.dbLocation,
           `--source-root=${sourceRoot}`,
-          "--calculate-language-specific-baseline",
+          ...baselineFilesOptions,
           "--extractor-include-aliases",
-          "--sublanguage-file-coverage",
           ...extraArgs,
           ...getExtraOptionsFromEnv(["database", "init"], {
-            ignoringOptions: ["--overwrite"]
+            ignoringOptions: ["--overwrite", ...baselineFilesOptions]
           })
         ],
         { stdin: externalRepositoryToken }
diff --git a/lib/upload-lib.js b/lib/upload-lib.js
index 72617ffde..9efe1fac5 100644
--- a/lib/upload-lib.js
+++ b/lib/upload-lib.js
@@ -91872,6 +91872,10 @@ async function getCodeQLForCmd(cmd, checkVersion) {
       } else if (overlayDatabaseMode === "overlay-base" /* OverlayBase */) {
         extraArgs.push("--overlay-base");
       }
+      const baselineFilesOptions = config.enableFileCoverageInformation ? [
+        "--calculate-language-specific-baseline",
+        "--sublanguage-file-coverage"
+      ] : ["--no-calculate-baseline"];
       await runCli(
         cmd,
         [
@@ -91881,12 +91885,11 @@ async function getCodeQLForCmd(cmd, checkVersion) {
           "--db-cluster",
           config.dbLocation,
           `--source-root=${sourceRoot}`,
-          "--calculate-language-specific-baseline",
+          ...baselineFilesOptions,
           "--extractor-include-aliases",
-          "--sublanguage-file-coverage",
           ...extraArgs,
           ...getExtraOptionsFromEnv(["database", "init"], {
-            ignoringOptions: ["--overwrite"]
+            ignoringOptions: ["--overwrite", ...baselineFilesOptions]
           })
         ],
         { stdin: externalRepositoryToken }
diff --git a/lib/upload-sarif-action.js b/lib/upload-sarif-action.js
index 3541f24ed..469329222 100644
--- a/lib/upload-sarif-action.js
+++ b/lib/upload-sarif-action.js
@@ -92422,6 +92422,10 @@ async function getCodeQLForCmd(cmd, checkVersion) {
       } else if (overlayDatabaseMode === "overlay-base" /* OverlayBase */) {
         extraArgs.push("--overlay-base");
       }
+      const baselineFilesOptions = config.enableFileCoverageInformation ? [
+        "--calculate-language-specific-baseline",
+        "--sublanguage-file-coverage"
+      ] : ["--no-calculate-baseline"];
       await runCli(
         cmd,
         [
@@ -92431,12 +92435,11 @@ async function getCodeQLForCmd(cmd, checkVersion) {
           "--db-cluster",
           config.dbLocation,
           `--source-root=${sourceRoot}`,
-          "--calculate-language-specific-baseline",
+          ...baselineFilesOptions,
           "--extractor-include-aliases",
-          "--sublanguage-file-coverage",
           ...extraArgs,
           ...getExtraOptionsFromEnv(["database", "init"], {
-            ignoringOptions: ["--overwrite"]
+            ignoringOptions: ["--overwrite", ...baselineFilesOptions]
           })
         ],
         { stdin: externalRepositoryToken }
diff --git a/src/codeql.ts b/src/codeql.ts
index 97f2f6028..c5c84f4d7 100644
--- a/src/codeql.ts
+++ b/src/codeql.ts
@@ -620,6 +620,13 @@ async function getCodeQLForCmd(
         extraArgs.push("--overlay-base");
       }
 
+      const baselineFilesOptions = config.enableFileCoverageInformation
+        ? [
+            "--calculate-language-specific-baseline",
+            "--sublanguage-file-coverage",
+          ]
+        : ["--no-calculate-baseline"];
+
       await runCli(
         cmd,
         [
@@ -631,12 +638,11 @@ async function getCodeQLForCmd(
           "--db-cluster",
           config.dbLocation,
           `--source-root=${sourceRoot}`,
-          "--calculate-language-specific-baseline",
+          ...baselineFilesOptions,
           "--extractor-include-aliases",
-          "--sublanguage-file-coverage",
           ...extraArgs,
           ...getExtraOptionsFromEnv(["database", "init"], {
-            ignoringOptions: ["--overwrite"],
+            ignoringOptions: ["--overwrite", ...baselineFilesOptions],
           }),
         ],
         { stdin: externalRepositoryToken },