diff --git a/src/gmt_init.c b/src/gmt_init.c
index 369ba06c940..9d5ed5adfac 100644
--- a/src/gmt_init.c
+++ b/src/gmt_init.c
@@ -16635,7 +16635,8 @@ void gmt_end_module (struct GMT_CTRL *GMT, struct GMT_CTRL *Ccopy) {
 		GMT->current.io.col[GMT_OUT][i].col = GMT->current.io.col[GMT_OUT][i].order = i;	/* Default order */
 
 	for (i = 0; i < 2; i++) GMT->current.io.skip_if_NaN[i] = true;								/* x/y must be non-NaN */
-	for (i = 0; i < 2; i++) gmt_set_column_type (GMT, GMT_IO, i, GMT_IS_UNKNOWN);	/* Must be told [or find out] what x/y are */
+	if (GMT->hidden.func_level == 0)	/* Only when top-level module ends. Doesn't affect CLI but useful for externals */
+		for (i = 0; i < 2; i++) gmt_set_column_type (GMT, GMT_IO, i, GMT_IS_UNKNOWN);	/* Must be told [or find out] what x/y are */
 	for (i = 2; i < GMT_MAX_COLUMNS; i++) gmt_set_column_type (GMT, GMT_IO, i, GMT_IS_FLOAT);	/* Other columns default to floats */
 	gmt_M_memset (GMT->current.io.col_set[GMT_X], GMT_MAX_COLUMNS, char);	/* This is the initial state of input columns - all available to be changed by modules */
 	gmt_M_memset (GMT->current.io.col_set[GMT_Y], GMT_MAX_COLUMNS, char);	/* This is the initial state of output columns - all available to be changed by modules */