diff --git a/pkgs/development/web/deno/default.nix b/pkgs/development/web/deno/default.nix
index 7749249695d..3a0583628f0 100644
--- a/pkgs/development/web/deno/default.nix
+++ b/pkgs/development/web/deno/default.nix
@@ -18,16 +18,16 @@ let
 in
 rustPlatform.buildRustPackage rec {
   pname = "deno";
-  version = "1.3.0";
+  version = "1.3.1";
 
   src = fetchFromGitHub {
     owner = "denoland";
     repo = pname;
     rev = "v${version}";
-    sha256 = "163qvxggdv4mr1r1nab4s5n2b74bji0iil4r4nmp6n2ghssyf01h";
+    sha256 = "1j5ajasng380p5a7nkk9ag5zp9ybwfz7b2z42lyk1wfg0pcd6j0r";
     fetchSubmodules = true;
   };
-  cargoSha256 = "11i00a92i2d6y2vj04wa6qbpsd351qcdy6a9ansq6n3928m9f2pk";
+  cargoSha256 = "0ba7afk4n7k170cqwy0gjc53vz6bjc176s9w1wln6yfhh55fyw6x";
 
   # Install completions post-install
   nativeBuildInputs = [ installShellFiles ];
diff --git a/pkgs/development/web/deno/update/common.ts b/pkgs/development/web/deno/update/common.ts
index 71e4d638f8d..d8956b21d16 100644
--- a/pkgs/development/web/deno/update/common.ts
+++ b/pkgs/development/web/deno/update/common.ts
@@ -8,7 +8,20 @@ const run = async (command: string, args: string[]) => {
     { cmd: [command, ...args], stdout: "piped", stderr: "piped" },
   );
   if (!(await cmd.status()).success) {
-    throw await cmd.stderrOutput().then((b) => decode(b));
+    const error = await cmd.stderrOutput().then((b) => decode(b).trimEnd());
+    // Known error we can ignore
+    if (error.includes("'allow-unsafe-native-code-during-evaluation'")) {
+      // Extract the target sha256 out of the error
+      const target = "  got:    sha256:";
+      const match = error
+        .split("\n")
+        .find((l) => l.includes(target))
+        ?.split(target)[1];
+      if (typeof match !== "undefined") {
+        return match;
+      }
+    }
+    throw new Error(error);
   }
   return cmd.output().then((b) => decode(b).trimEnd());
 };