diff --git a/pkgs/by-name/go/go-toml/package.nix b/pkgs/by-name/go/go-toml/package.nix
index e18ac104f70d..5ea5e58c51ea 100644
--- a/pkgs/by-name/go/go-toml/package.nix
+++ b/pkgs/by-name/go/go-toml/package.nix
@@ -25,10 +25,6 @@ buildGoModule {
     "cmd/tomltestgen"
   ];
 
-  # allowGoReference adds the flag `-trimpath` which is also denoted by, go-toml's goreleaser config
-  #  <https://github.com/pelletier/go-toml/blob/a3d5a0bb530b5206c728eed9cb57323061922bcb/.goreleaser.yaml#L13>
-  allowGoReference = true;
-
   ldflags = [
     "-s"
     "-w"
diff --git a/pkgs/pkgs-lib/formats.nix b/pkgs/pkgs-lib/formats.nix
index 9478a11f83f6..0e0c9368fab1 100644
--- a/pkgs/pkgs-lib/formats.nix
+++ b/pkgs/pkgs-lib/formats.nix
@@ -461,16 +461,18 @@ optionalAttrs allowAliases aliases
       generate =
         name: value:
         pkgs.callPackage (
-          { runCommand, yj }:
+          { runCommand, go-toml }:
           runCommand name
             {
-              nativeBuildInputs = [ yj ];
+              nativeBuildInputs = [ go-toml ];
               value = builtins.toJSON value;
               passAsFile = [ "value" ];
               preferLocalBuild = true;
             }
+            # -use-json-number: preserve JSON ints as TOML ints
+            # (Go's json.Decoder defaults to float64 for all numbers)
             ''
-              yj -jt < "$valuePath" > "$out"
+              jsontoml -use-json-number < "$valuePath" > "$out"
             ''
         ) { };
 
diff --git a/pkgs/pkgs-lib/tests/formats.nix b/pkgs/pkgs-lib/tests/formats.nix
index d51b5d2f272b..49b9ac4c8a30 100644
--- a/pkgs/pkgs-lib/tests/formats.nix
+++ b/pkgs/pkgs-lib/tests/formats.nix
@@ -695,16 +695,51 @@ runBuildTests {
       float = 3.141
       int = 10
       list = [1, 2]
-      str = "foo"
+      str = 'foo'
       true = true
 
       [attrs]
-      foo = "foo"
+      foo = 'foo'
 
       [level1]
       [level1.level2]
       [level1.level2.level3]
-      level4 = "deep"
+      level4 = 'deep'
+    '';
+  };
+
+  # Regression test for https://github.com/NixOS/nixpkgs/issues/511970
+  # yj crashes on arrays mixing scalars and attrsets (heterogeneous arrays),
+  # e.g. Helix language-server configs like ["bash-ls", {name = "ts-ls"; ...}].
+  # TOML 1.0 allows mixed-type arrays; the converter must emit them as
+  # inline arrays with inline tables.
+  tomlHeterogeneousArray = shouldPass {
+    format = formats.toml { };
+    input = {
+      language-server = [
+        "bash-language-server"
+        {
+          name = "typescript-language-server";
+          except-features = [ "diagnostics" ];
+        }
+      ];
+    };
+    expected = ''
+      language-server = ['bash-language-server', {except-features = ['diagnostics'], name = 'typescript-language-server'}]
+    '';
+  };
+
+  # Regression test for https://github.com/sclevine/yj/issues/52
+  # yj truncates keys at the first comma because it stores TOML keys in Go
+  # struct tags, where commas are option separators.
+  # e.g. "stack(x,n)" is emitted as "stack(x" — silently losing data.
+  tomlCommaInKey = shouldPass {
+    format = formats.toml { };
+    input = {
+      "stack(x,n)" = "foobar";
+    };
+    expected = ''
+      'stack(x,n)' = 'foobar'
     '';
   };