diff --git a/docs/sphinx/source/whatsnew/v0.13.1.rst b/docs/sphinx/source/whatsnew/v0.13.1.rst
index 2109b117d5..84dfaf0a9d 100644
--- a/docs/sphinx/source/whatsnew/v0.13.1.rst
+++ b/docs/sphinx/source/whatsnew/v0.13.1.rst
@@ -16,7 +16,8 @@ Deprecations
 
 Bug fixes
 ~~~~~~~~~
-
+* Fix :py:func:`~pvlib.clearsky.detect_clearsky` to use inferred window length when
+  ``infer_limits=True``. (:issue:`2542`, :pull:`2550`)
 
 Enhancements
 ~~~~~~~~~~~~
@@ -74,3 +75,4 @@ Contributors
 * Rodrigo Amaro e Silva (:ghuser:`ramaroesilva`)
 * Kevin Anderson (:ghuser:`kandersolar`)
 * Mikaella Brewer (:ghuser:`brwerx`)
+* Will Holmgren (:ghuser:`wholmgren`)
diff --git a/pvlib/clearsky.py b/pvlib/clearsky.py
index be75ecd47a..8cc867e020 100644
--- a/pvlib/clearsky.py
+++ b/pvlib/clearsky.py
@@ -818,22 +818,31 @@ def detect_clearsky(measured, clearsky, times=None, infer_limits=False,
     sample_interval, samples_per_window = \
         tools._get_sample_intervals(times, window_length)
 
-    if samples_per_window < 3:
-        raise ValueError(f"Samples per window of {samples_per_window}"
-                         " found. Each window must contain at least 3 data"
-                         " points."
-                         f" Window length of {window_length} found; increase"
-                         f" window length to {3*sample_interval} or longer.")
-
     # if infer_limits, find threshold values using the sample interval
     if infer_limits:
-        window_length, mean_diff, max_diff, lower_line_length, \
-            upper_line_length, var_diff, slope_dev = \
-                _clearsky_get_threshold(sample_interval)
+        (
+            window_length,
+            mean_diff,
+            max_diff,
+            lower_line_length,
+            upper_line_length,
+            var_diff,
+            slope_dev,
+        ) = _clearsky_get_threshold(sample_interval)
 
         # recalculate samples_per_window using returned window_length
-        _, samples_per_window = \
-            tools._get_sample_intervals(times, window_length)
+        sample_interval, samples_per_window = tools._get_sample_intervals(
+            times, window_length
+        )
+
+    if samples_per_window < 3:
+        raise ValueError(
+            f"Samples per window of {samples_per_window}"
+            " found. Each window must contain at least 3 data"
+            " points."
+            f" Window length of {window_length} found. Increase"
+            f" window length to {3 * sample_interval} or longer."
+        )
 
     # check that we have enough data to produce a nonempty hankel matrix
     if len(times) < samples_per_window:
diff --git a/tests/test_clearsky.py b/tests/test_clearsky.py
index 0ef5dfeacd..296b96b345 100644
--- a/tests/test_clearsky.py
+++ b/tests/test_clearsky.py
@@ -688,6 +688,14 @@ def test_detect_clearsky_window_too_short(detect_clearsky_data):
         clearsky.detect_clearsky(expected['GHI'], cs['ghi'], window_length=2)
 
 
+def test_detect_clearsky_infer_checks(detect_clearsky_threshold_data):
+    # GH 2542
+    expected, cs = detect_clearsky_threshold_data
+    expected = expected.resample('10min').mean()
+    cs = cs.resample('10min').mean()
+    clearsky.detect_clearsky(expected['GHI'], cs['ghi'], infer_limits=True)
+
+
 @pytest.mark.parametrize("window_length", [5, 10, 15, 20, 25])
 def test_detect_clearsky_optimizer_not_failed(
     detect_clearsky_data, window_length