diff --git a/build.lua b/build.lua
index 3d2e0ca93..9daaba0a8 100644
--- a/build.lua
+++ b/build.lua
@@ -35,7 +35,15 @@ specialformats["latex"] = specialformats["latex"] or
 checkengines = {"pdftex", "latexdvips", "latexdvisvgm", "luatex", "xetex"}
 
 -- Use multiple sets of tests
-checkconfigs = { "build", "config-gd", "config-manual" }
+checkconfigs = {
+  "build",
+  "config-gd",
+  "config-manual",
+  "config-shell",
+}
+
+-- common testing support files
+checksuppfiles = {"pgf-regression-test.tex"}
 
 -- For release
 ctanzip = "pgf.ctan.flatdir"
diff --git a/config-shell.lua b/config-shell.lua
new file mode 100644
index 000000000..f22092edd
--- /dev/null
+++ b/config-shell.lua
@@ -0,0 +1,7 @@
+-- Tests which require shell escape enabled
+
+testfiledir  = "testfiles-shell"
+checkopts    = "-interaction=nonstopmode -shell-escape"
+
+-- files removed between different engine tests
+dynamicfiles = {"*.gnuplot", "*.table"}
diff --git a/doc/generic/pgf/CHANGELOG.md b/doc/generic/pgf/CHANGELOG.md
index 3eabe0278..f32fcb720 100644
--- a/doc/generic/pgf/CHANGELOG.md
+++ b/doc/generic/pgf/CHANGELOG.md
@@ -9,6 +9,11 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
 ### Fixed
 
 - Fix formatting of `default XXX, initially XXX` in key docs #1278
+- Correct the fix to trim spaces from `gnuplot` functions #1397 #1399
+
+### Added
+
+- Emulated `runsystem(...)` logging for LuaTeX
 
 ## [3.1.11] - 2025-08-14 Henri Menke
 
diff --git a/testfiles/support/pgf-regression-test.tex b/support/pgf-regression-test.tex
similarity index 100%
rename from testfiles/support/pgf-regression-test.tex
rename to support/pgf-regression-test.tex
diff --git a/testfiles-shell/gh1397.lvt b/testfiles-shell/gh1397.lvt
new file mode 100644
index 000000000..f4b6768bb
--- /dev/null
+++ b/testfiles-shell/gh1397.lvt
@@ -0,0 +1,51 @@
+\documentclass{article}
+\input{pgf-regression-test}
+
+\usepackage{tikz}
+
+\begin{document}
+
+\START
+
+\BEGINTEST{no .gnuplot}
+\begin{tikzpicture}
+  \draw[id=normal] plot[domain=-2:2] function {x**2};
+\end{tikzpicture}
+
+\SHOWFILE{\jobname.normal.gnuplot}
+\ENDTEST
+
+\BEGINTEST{no .gnuplot, leading space in function}
+\begin{tikzpicture}
+  \draw[id=leading-space] plot[domain=-2:2] function { x**2};
+\end{tikzpicture}
+
+\SHOWFILE{\jobname.leading-space.gnuplot}
+\ENDTEST
+
+\BEGINTEST{no .gnuplot, trailing space in function}
+\begin{tikzpicture}
+  \draw[id=trailing-space] plot[domain=-2:2] function {x**2 };
+\end{tikzpicture}
+
+\SHOWFILE{\jobname.trailing-space.gnuplot}
+\ENDTEST
+
+\BEGINTEST{.gnuplot existing and matched}
+\begin{tikzpicture}
+  \draw[id=normal] plot[domain=-2:2] function {x**2};
+  \draw[id=leading-space] plot[domain=-2:2] function { x**2};
+  \draw[id=trailing-space] plot[domain=-2:2] function {x**2 };
+\end{tikzpicture}
+\ENDTEST
+
+\BEGINTEST{.gnuplot existing but outdated}
+\begin{tikzpicture}
+  % use the existing id but a different domain
+  \draw[id=normal] plot[domain=-4:4] function {x**2};
+\end{tikzpicture}
+
+\SHOWFILE{\jobname.normal.gnuplot}
+\ENDTEST
+
+\END
diff --git a/testfiles-shell/gh1397.tlg b/testfiles-shell/gh1397.tlg
new file mode 100644
index 000000000..11a2b8f7b
--- /dev/null
+++ b/testfiles-shell/gh1397.tlg
@@ -0,0 +1,42 @@
+This is a generated file for the l3build validation system.
+Don't change this file in any respect.
+============================================================
+TEST 1: no .gnuplot
+============================================================
+runsystem(gnuplot gh1397.normal.gnuplot)...executed.
+-------- gh1397.normal.gnuplot (start) ---------
+(gh1397.normal.gnuplot) set table "gh1397.normal.table"; set format "%.5f"[nl]
+set samples 25; plot [x=-2:2] x**2[nl]
+-------- gh1397.normal.gnuplot (end) -----------
+============================================================
+============================================================
+TEST 2: no .gnuplot, leading space in function
+============================================================
+runsystem(gnuplot gh1397.leading-space.gnuplot)...executed.
+-------- gh1397.leading-space.gnuplot (start) ---------
+(gh1397.leading-space.gnuplot) set table "gh1397.leading-space.table"; set format "%.5f"[nl]
+set samples 25; plot [x=-2:2] x**2[nl]
+-------- gh1397.leading-space.gnuplot (end) -----------
+============================================================
+============================================================
+TEST 3: no .gnuplot, trailing space in function
+============================================================
+runsystem(gnuplot gh1397.trailing-space.gnuplot)...executed.
+-------- gh1397.trailing-space.gnuplot (start) ---------
+(gh1397.trailing-space.gnuplot) set table "gh1397.trailing-space.table"; set format "%.5f"[nl]
+set samples 25; plot [x=-2:2] x**2[nl]
+-------- gh1397.trailing-space.gnuplot (end) -----------
+============================================================
+============================================================
+TEST 4: .gnuplot existing and matched
+============================================================
+============================================================
+============================================================
+TEST 5: .gnuplot existing but outdated
+============================================================
+runsystem(gnuplot gh1397.normal.gnuplot)...executed.
+-------- gh1397.normal.gnuplot (start) ---------
+(gh1397.normal.gnuplot) set table "gh1397.normal.table"; set format "%.5f"[nl]
+set samples 25; plot [x=-4:4] x**2[nl]
+-------- gh1397.normal.gnuplot (end) -----------
+============================================================
diff --git a/tex/generic/pgf/modules/pgfmoduleplot.code.tex b/tex/generic/pgf/modules/pgfmoduleplot.code.tex
index 4dbaa14f0..1b070a89a 100644
--- a/tex/generic/pgf/modules/pgfmoduleplot.code.tex
+++ b/tex/generic/pgf/modules/pgfmoduleplot.code.tex
@@ -481,6 +481,7 @@
   \pgfutilpreparefilename{#1.table}%
   \let\pgf@plottablefile=\pgfretval
   \let\pgf@plottablefile@quoted=\pgfretvalquoted
+  \edef\pgf@plot@code{\pgfutil@trimspaces@e{#2}}%
   \begingroup
   \endlinechar=-1 % suppress white space at end
   % Check, whether it is up-to-date
@@ -490,7 +491,6 @@
     \pgfutil@read\pgfutil@inputcheck to\pgf@temp% ignored
     \pgfutil@read\pgfutil@inputcheck to\pgf@plot@line%
     \closein\pgfutil@inputcheck
-    \edef\pgf@plot@code{\pgfutil@trimspaces@e{#2}}%
     \ifx\pgf@plot@code\pgf@plot@line%
       \openin\pgfutil@inputcheck=\pgfretval\relax
       \ifeof\pgfutil@inputcheck%
diff --git a/tex/generic/pgf/utilities/pgfutil-common.tex b/tex/generic/pgf/utilities/pgfutil-common.tex
index 66c6fd015..c12cf5d32 100644
--- a/tex/generic/pgf/utilities/pgfutil-common.tex
+++ b/tex/generic/pgf/utilities/pgfutil-common.tex
@@ -883,9 +883,22 @@
   \def\pgfutil@luaescapestring#1{}
 \fi
 
-
+% Emulate the "runsystem(...)" logging for LuaTeX
+% based on the emulation in l3kernel (l3sys.dtx, @@_shell_now:e), and the
+% ending periods are added following https://github.com/latex3/latex2e/commit/90d53de44fe4a09baa4a17506abe6ce9e120a7c3.
 \def\pgfutil@shellescape@lua@eightseven#1{%
-    \pgfutil@directlua{os.execute("\pgfutil@luaescapestring{#1}")}%
+    \pgfutil@directlua{%
+        local write_nl = texio.write_nl
+        local cmd = "\pgfutil@luaescapestring{#1}"
+        local status, msg = os.execute(cmd)
+        if status == nil then
+            write_nl("log", "runsystem(" .. cmd .. ")...(" .. msg .. ").\string\n")
+        elseif status == 0 then
+            write_nl("log", "runsystem(" .. cmd .. ")...executed.\string\n")
+        else
+            write_nl("log", "runsystem(" .. cmd .. ")...failed. " .. (msg or "") .. "\string\n")
+        end
+    }%
 }%
 \def\pgfutil@shellescape#1{%
     \immediate\write18{#1}%