diff --git a/bashate/bashate.py b/bashate/bashate.py
index 47f0ad2..522f202 100755
--- a/bashate/bashate.py
+++ b/bashate/bashate.py
@@ -320,7 +320,18 @@ def check_files(self, files, verbose, max_line_length=79):
             # syntax errors when you try to run them.
             check_syntax(fname, report)
 
+            # Remember the last raw line of this file (and where it
+            # was) so we can check it for a trailing newline once the
+            # file is exhausted.  "line" itself is unusable for that:
+            # it gets rewritten by inline-comment stripping and by the
+            # logical_line loop below.
+            last_line = None
+            last_lineno = None
+
             for line in fileinput.input(fname):
+                last_line = line
+                last_lineno = fileinput.filelineno()
+
                 if fileinput.isfirstline():
 
                     check_hashbang(line, fileinput.filename(), report)
@@ -408,11 +419,17 @@ def check_files(self, files, verbose, max_line_length=79):
                     check_bare_arithmetic(line, report)
                     check_conditional_expression(line, report)
 
-        # finished processing the file
-
-        # last line should always end with a newline
-        if not line.endswith('\n'):
-            report.print_error(MESSAGES['E004'].msg, line)
+            # finished processing the file
+
+            # last line should always end with a newline.  Note this
+            # must be inside the "for fname in files" loop: checking
+            # it after all files have been processed only ever
+            # examines whichever file happened to be scanned last.
+            # Pass filename/filelineno explicitly because fileinput
+            # has been exhausted by now and no longer reports them.
+            if last_line is not None and not last_line.endswith('\n'):
+                report.print_error(MESSAGES['E004'].msg, last_line,
+                                   filename=fname, filelineno=last_lineno)
 
 
 def main(args=None):
diff --git a/bashate/tests/samples/E004_bad2.sh b/bashate/tests/samples/E004_bad2.sh
new file mode 100644
index 0000000..973339e
--- /dev/null
+++ b/bashate/tests/samples/E004_bad2.sh
@@ -0,0 +1,3 @@
+#!/bin/bash
+
+echo "this file also has no newline at end"
\ No newline at end of file
diff --git a/bashate/tests/test_bashate.py b/bashate/tests/test_bashate.py
index 27e4943..30515fc 100644
--- a/bashate/tests/test_bashate.py
+++ b/bashate/tests/test_bashate.py
@@ -160,6 +160,36 @@ def test_sample_E004_bad(self):
         self.run.check_files(test_files, False)
         self.assert_error_found('E004', 3)
 
+    def test_sample_E004_bad_multiple_files(self):
+        # E004 must be reported for every offending file, not just
+        # whichever one happens to be scanned last.
+        test_files = ['bashate/tests/samples/E004_bad.sh',
+                      'bashate/tests/samples/E004_bad2.sh']
+        self.run.check_files(test_files, False)
+        self.assert_error_found('E004', 3)
+        self.assertEqual(2, self.run.error_count)
+
+    def test_sample_E004_bad_followed_by_good(self):
+        # A file missing its trailing newline must still be reported
+        # when a well-formed file is scanned after it.
+        test_files = ['bashate/tests/samples/E004_bad.sh',
+                      'bashate/tests/samples/E003_good.sh']
+        self.run.check_files(test_files, False)
+        self.assert_error_found('E004', 3)
+        self.assertEqual(1, self.run.error_count)
+
+    def test_sample_E004_good_not_flagged(self):
+        # A file that does end with a newline must not be flagged,
+        # even when scanned after one that does not.
+        test_files = ['bashate/tests/samples/E004_bad.sh',
+                      'bashate/tests/samples/E003_good.sh']
+        self.run.check_files(test_files, False)
+        for call in self.m_log_error.call_args_list:
+            args = call[0]
+            if args[0].startswith('E004'):
+                self.assertEqual('bashate/tests/samples/E004_bad.sh',
+                                 args[2])
+
     def test_sample_E006_bad(self):
         test_files = ['bashate/tests/samples/E006_bad.sh']
         self.run.check_files(test_files, False)
diff --git a/releasenotes/notes/fix-e004-per-file-fc12fe9acd699cba.yaml b/releasenotes/notes/fix-e004-per-file-fc12fe9acd699cba.yaml
new file mode 100644
index 0000000..902b1da
--- /dev/null
+++ b/releasenotes/notes/fix-e004-per-file-fc12fe9acd699cba.yaml
@@ -0,0 +1,14 @@
+---
+fixes:
+  - |
+    ``E004`` (file did not end with a newline) is now checked once per
+    file, rather than once per ``bashate`` invocation.  Previously the
+    check ran after every file had been processed, so only whichever
+    file happened to be scanned last was examined; a file missing its
+    trailing newline went unreported whenever another file followed it
+    on the command line.
+
+    This particularly affected callers that batch files into a single
+    invocation, such as `pre-commit.com <https://pre-commit.com>`__,
+    where the same offending file could pass or fail depending only on
+    how the file list happened to be ordered.