diff --git a/Makefile.inc1 b/Makefile.inc1
--- a/Makefile.inc1
+++ b/Makefile.inc1
@@ -1021,7 +1021,8 @@
 .endif
 
 .if make(distributeworld)
-CERTCTLDESTDIR=	${DESTDIR}/${DISTDIR}/base
+CERTCTLDESTDIR=	${DESTDIR}/${DISTDIR}
+CERTCTLFLAGS+=	-d /base
 .else
 CERTCTLDESTDIR=	${DESTDIR}
 .endif
diff --git a/usr.sbin/certctl/certctl.8 b/usr.sbin/certctl/certctl.8
--- a/usr.sbin/certctl/certctl.8
+++ b/usr.sbin/certctl/certctl.8
@@ -63,6 +63,8 @@
 command.
 .It Fl D Ar destdir
 Specify the DESTDIR (overriding values from the environment).
+.It Fl d Ar distbase
+Specify the DISTBASE (overriding values from the environment).
 .It Fl l
 When listing installed (trusted or untrusted) certificates, show the
 full path and distinguished name for each certificate.
@@ -118,6 +120,8 @@
 .Bl -tag -width UNTRUSTDESTDIR
 .It Ev DESTDIR
 Alternate destination directory to operate on.
+.It Ev DISTBASE
+Additional path component to include when operating on certificate directories.
 .It Ev LOCALBASE
 Location for local programs.
 Defaults to the value of the user.localbase sysctl which is usually
@@ -125,22 +129,22 @@
 .It Ev TRUSTPATH
 List of paths to search for trusted certificates.
 Default:
-.Pa ${DESTDIR}/usr/share/certs/trusted
-.Pa ${DESTDIR}${LOCALBASE}/share/certs/trusted
-.Pa ${DESTDIR}${LOCALBASE}/share/certs
+.Pa ${DESTDIR}${DISTBASE}/usr/share/certs/trusted
+.Pa ${DESTDIR}${DISTBASE}${LOCALBASE}/share/certs/trusted
+.Pa ${DESTDIR}${DISTBASE}${LOCALBASE}/share/certs
 .It Ev UNTRUSTPATH
 List of paths to search for untrusted certificates.
 Default:
-.Pa ${DESTDIR}/usr/share/certs/untrusted
-.Pa ${DESTDIR}${LOCALBASE}/share/certs/untrusted
+.Pa ${DESTDIR}${DISTBASE}/usr/share/certs/untrusted
+.Pa ${DESTDIR}${DISTBASE}${LOCALBASE}/share/certs/untrusted
 .It Ev TRUSTDESTDIR
 Destination directory for symbolic links to trusted certificates.
 Default:
-.Pa ${DESTDIR}/etc/ssl/certs
+.Pa ${DESTDIR}${DISTBASE}/etc/ssl/certs
 .It Ev UNTRUSTDESTDIR
 Destination directory for symbolic links to untrusted certificates.
 Default:
-.Pa ${DESTDIR}/etc/ssl/untrusted
+.Pa ${DESTDIR}${DISTBASE}/etc/ssl/untrusted
 .It Ev BUNDLE
 File name of bundle to produce.
 .El
diff --git a/usr.sbin/certctl/certctl.c b/usr.sbin/certctl/certctl.c
--- a/usr.sbin/certctl/certctl.c
+++ b/usr.sbin/certctl/certctl.c
@@ -63,6 +63,7 @@
 
 static const char *localbase;
 static const char *destdir;
+static const char *distbase;
 static const char *metalog;
 
 static const char *uname = "root";
@@ -124,14 +125,14 @@
 }
 
 /*
- * Expand %L into LOCALBASE and prefix DESTDIR.
+ * Expand %L into LOCALBASE and prefix DESTDIR and DISTBASE.
  */
 static char *
 expand_path(const char *template)
 {
 	if (template[0] == '%' && template[1] == 'L')
 		return (xasprintf("%s%s%s", destdir, localbase, template + 2));
-	return (xasprintf("%s%s", destdir, template));
+	return (xasprintf("%s%s%s", destdir, distbase, template));
 }
 
 /*
@@ -155,6 +156,9 @@
 /*
  * If destdir is a prefix of path, returns a pointer to the rest of path,
  * otherwise returns path.
+ *
+ * Note that this intentionally does not strip distbase from the path!
+ * Unlike destdir, distbase is expected to be included in the metalog.
  */
 static const char *
 unexpand_path(const char *path)
@@ -488,9 +492,10 @@
 			free(tmppath);
 			tmppath = NULL;
 		}
+		fflush(f);
 		/* emit metalog */
 		if (mlf != NULL) {
-			fprintf(mlf, "%s/%s type=file "
+			fprintf(mlf, ".%s/%s type=file "
 			    "uname=%s gname=%s mode=%#o size=%ld\n",
 			    unexpand_path(dir), path,
 			    uname, gname, mode, ftell(f));
@@ -561,7 +566,7 @@
 	}
 	if (ret == 0 && mlf != NULL) {
 		fprintf(mlf,
-		    "%s/%s type=file uname=%s gname=%s mode=%#o size=%ld\n",
+		    ".%s/%s type=file uname=%s gname=%s mode=%#o size=%ld\n",
 		    unexpand_path(dir), file, uname, gname, mode, ftell(f));
 	}
 	fclose(f);
@@ -905,7 +910,7 @@
 set_defaults(void)
 {
 	const char *value;
-	char *str;
+	char *end, *str;
 	size_t len;
 
 	if (localbase == NULL &&
@@ -925,6 +930,15 @@
 	if (destdir == NULL &&
 	    (destdir = getenv("DESTDIR")) == NULL)
 		destdir = "";
+	/* strip trailing slashes */
+	end = strchrnul(destdir, '\0');
+	while (end > destdir + 1 && *(end - 1) == '/')
+		end--;
+	*end = '\0';
+
+	if (distbase == NULL &&
+	    (distbase = getenv("DISTBASE")) == NULL)
+		distbase = "";
 
 	if (unprivileged && metalog == NULL &&
 	    (metalog = getenv("METALOG")) == NULL)
@@ -966,6 +980,7 @@
 
 	info("localbase:\t%s", localbase);
 	info("destdir:\t%s", destdir);
+	info("distbase:\t%s", distbase);
 	info("unprivileged:\t%s", unprivileged ? "true" : "false");
 	info("verbose:\t%s", verbose ? "true" : "false");
 }
@@ -987,11 +1002,11 @@
 static void
 usage(void)
 {
-	fprintf(stderr, "usage: certctl [-lv] [-D destdir] list\n"
-	    "       certctl [-lv] [-D destdir] untrusted\n"
-	    "       certctl [-BnUv] [-D destdir] [-M metalog] rehash\n"
-	    "       certctl [-nv] [-D destdir] untrust <file>\n"
-	    "       certctl [-nv] [-D destdir] trust <file>\n");
+	fprintf(stderr, "usage: certctl [-lv] [-D destdir] [-d distbase] list\n"
+	    "       certctl [-lv] [-D destdir] [-d distbase] untrusted\n"
+	    "       certctl [-BnUv] [-D destdir] [-d distbase] [-M metalog] rehash\n"
+	    "       certctl [-nv] [-D destdir] [-d distbase] untrust <file>\n"
+	    "       certctl [-nv] [-D destdir] [-d distbase] trust <file>\n");
 	exit(1);
 }
 
@@ -1001,7 +1016,7 @@
 	const char *command;
 	int opt;
 
-	while ((opt = getopt(argc, argv, "BcD:g:lL:M:no:Uv")) != -1)
+	while ((opt = getopt(argc, argv, "BcD:d:g:lL:M:no:Uv")) != -1)
 		switch (opt) {
 		case 'B':
 			nobundle = true;
@@ -1012,6 +1027,9 @@
 		case 'D':
 			destdir = optarg;
 			break;
+		case 'd':
+			distbase = optarg;
+			break;
 		case 'g':
 			gname = optarg;
 			break;
diff --git a/usr.sbin/certctl/tests/certctl_test.sh b/usr.sbin/certctl/tests/certctl_test.sh
--- a/usr.sbin/certctl/tests/certctl_test.sh
+++ b/usr.sbin/certctl/tests/certctl_test.sh
@@ -65,36 +65,50 @@
 	export DESTDIR="$PWD"
 
 	# Create input directories
-	mkdir -p usr/share/certs/trusted
-	mkdir -p usr/share/certs/untrusted
-	mkdir -p usr/local/share/certs
+	mkdir -p ${DESTDIR}${DISTBASE}/usr/share/certs/trusted
+	mkdir -p ${DESTDIR}${DISTBASE}/usr/share/certs/untrusted
+	mkdir -p ${DESTDIR}/usr/local/share/certs
 
 	# Create output directories
-	mkdir -p etc/ssl/certs
-	mkdir -p etc/ssl/untrusted
+	mkdir -p ${DESTDIR}${DISTBASE}/etc/ssl/certs
+	mkdir -p ${DESTDIR}${DISTBASE}/etc/ssl/untrusted
 
 	# Generate a random key
 	keyname="testkey"
 	gen_key ${keyname}
 
 	# Generate certificates
+	:>metalog.expect
+	metalog() {
+		echo ".${DISTBASE}$@ type=file" >>metalog.expect
+	}
 	set1 | while read crtname hash ; do
 		gen_crt ${crtname} ${keyname}
-		mv ${crtname}.crt usr/share/certs/trusted
+		mv ${crtname}.crt ${DESTDIR}${DISTBASE}/usr/share/certs/trusted
+		metalog "/etc/ssl/certs/${hash}.0"
 	done
+	local c=0
 	coll | while read crtname hash ; do
 		gen_crt ${crtname} ${keyname}
-		mv ${crtname}.crt usr/share/certs/trusted
+		mv ${crtname}.crt ${DESTDIR}${DISTBASE}/usr/share/certs/trusted
+		metalog "/etc/ssl/certs/${hash}.${c}"
+		c=$((c+1))
 	done
 	set2 | while read crtname hash ; do
 		gen_crt ${crtname} ${keyname}
 		openssl x509 -in ${crtname}.crt
 		rm ${crtname}.crt
+		metalog "/etc/ssl/certs/${hash}.0"
 	done >usr/local/share/certs/bundle.crt
 	set3 | while read crtname hash ; do
 		gen_crt ${crtname} ${keyname}
-		mv ${crtname}.crt usr/share/certs/untrusted
+		mv ${crtname}.crt ${DESTDIR}${DISTBASE}/usr/share/certs/untrusted
+		metalog "/etc/ssl/untrusted/${hash}.0"
 	done
+	metalog "/etc/ssl/cert.pem"
+	unfunction metalog
+	sort metalog.expect >metalog.expect.sorted
+	mv metalog.expect.sorted metalog.expect
 }
 
 check_trusted() {
@@ -102,12 +116,12 @@
 	local subject="$(subject ${crtname})"
 	local c=${2:-1}
 
-	atf_check -o match:"found: ${c}\$" \
+	atf_check -e ignore -o match:"found: ${c}\$" \
 	    openssl storeutl -noout -subject "${subject}" \
-	    etc/ssl/certs
-	atf_check -o match:"found: 0\$" \
+	    ${DESTDIR}${DISTBASE}/etc/ssl/certs
+	atf_check -e ignore -o not-match:"found: [1-9]"  \
 	    openssl storeutl -noout -subject "${subject}" \
-	    etc/ssl/untrusted
+	    ${DESTDIR}${DISTBASE}/etc/ssl/untrusted
 }
 
 check_untrusted() {
@@ -115,23 +129,25 @@
 	local subject="$(subject ${crtname})"
 	local c=${2:-1}
 
-	atf_check -o match:"found: 0\$" \
+	atf_check -e ignore -o not-match:"found: [1-9]" \
 	    openssl storeutl -noout -subject "${subject}" \
-	    etc/ssl/certs
-	atf_check -o match:"found: ${c}\$" \
+	    ${DESTDIR}/${DISTBASE}/etc/ssl/certs
+	atf_check -e ignore -o match:"found: ${c}\$" \
 	    openssl storeutl -noout -subject "${subject}" \
-	    etc/ssl/untrusted
+	    ${DESTDIR}/${DISTBASE}/etc/ssl/untrusted
 }
 
 check_in_bundle() {
+	local b=${DISTBASE}${DISTBASE+/}
 	local crtfile=$1
 	local line
 
 	line=$(tail +5 "${crtfile}" | head -1)
-	atf_check grep -q "${line}" etc/ssl/cert.pem
+	atf_check grep -q "${line}" ${DESTDIR}${DISTBASE}/etc/ssl/cert.pem
 }
 
 check_not_in_bundle() {
+	local b=${DISTBASE}${DISTBASE+/}
 	local crtfile=$1
 	local line
 
@@ -150,7 +166,7 @@
 	atf_check certctl rehash
 
 	# Verify non-colliding trusted certificates
-	(set1 ; set2) > trusted
+	(set1; set2) >trusted
 	while read crtname hash ; do
 		check_trusted "${crtname}"
 	done <trusted
@@ -167,7 +183,7 @@
 		check_untrusted "${crtname}"
 	done <untrusted
 
-	# Verify bundle; storeutl is no help here
+	# Verify bundle
 	for f in etc/ssl/certs/*.? ; do
 		check_in_bundle "${f}"
 	done
@@ -213,9 +229,41 @@
 	check_not_in_bundle ${crtfile}
 }
 
+atf_test_case metalog
+metalog_head()
+{
+	atf_set "descr" "Verify the metalog"
+}
+metalog_body()
+{
+	export DISTBASE=/base
+	certctl_setup
+
+	# certctl gets DESTDIR and DISTBASE from environment
+	rm -f metalog.orig
+	atf_check certctl -U -M metalog.orig rehash
+	sed -E 's/(type=file) .*/\1/' metalog.orig | sort >metalog.short
+	atf_check diff -u metalog.expect metalog.short
+
+	# certctl gets DESTDIR and DISTBASE from command line
+	rm -f metalog.orig
+	atf_check env -uDESTDIR -uDISTBASE \
+	    certctl -D ${DESTDIR} -d ${DISTBASE} -U -M metalog.orig rehash
+	sed -E 's/(type=file) .*/\1/' metalog.orig | sort >metalog.short
+	atf_check diff -u metalog.expect metalog.short
+
+	# as above, but intentionally add trailing slash to DESTDIR
+	rm -f metalog.orig
+	atf_check env -uDESTDIR -uDISTBASE \
+	    certctl -D ${DESTDIR}/ -d ${DISTBASE} -U -M metalog.orig rehash
+	sed -E 's/(type=file) .*/\1/' metalog.orig | sort >metalog.short
+	atf_check diff -u metalog.expect metalog.short
+}
+
 atf_init_test_cases()
 {
 	atf_add_test_case rehash
 	atf_add_test_case trust
 	atf_add_test_case untrust
+	atf_add_test_case metalog
 }