diff --git a/sci-biology/hmmer/hmmer-2.3.2-r6.ebuild b/sci-biology/hmmer/hmmer-2.3.2-r6.ebuild
index 74a8a151b0c44..7766710967f5d 100644
--- a/sci-biology/hmmer/hmmer-2.3.2-r6.ebuild
+++ b/sci-biology/hmmer/hmmer-2.3.2-r6.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2024 Gentoo Authors
+# Copyright 1999-2025 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=8
 
-inherit flag-o-matic toolchain-funcs
+inherit dot-a flag-o-matic toolchain-funcs
 
 DESCRIPTION="Sequence analysis using profile hidden Markov models"
 HOMEPAGE="http://hmmer.org/"
@@ -27,6 +27,8 @@ src_configure() {
 	# required to expose pthread_setconcurrency(), #882279
 	append-cppflags -D_XOPEN_SOURCE=500
 
+	lto-guarantee-fat
+
 	# prevent stray environmental variable
 	# from causing issues in the test phase
 	unset TMPDIR
@@ -53,6 +55,8 @@ src_install() {
 	insinto /usr/include/hmmer2
 	doins squid/*.h
 
+	strip-lto-bytecode
+
 	dodoc NOTES Userguide.pdf
 	newdoc 00README README
 
diff --git a/sci-biology/hmmer/hmmer-3.1_beta2-r1.ebuild b/sci-biology/hmmer/hmmer-3.1_beta2-r1.ebuild
index 666d21cd5532e..22c366c1454e8 100644
--- a/sci-biology/hmmer/hmmer-3.1_beta2-r1.ebuild
+++ b/sci-biology/hmmer/hmmer-3.1_beta2-r1.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2022 Gentoo Authors
+# Copyright 1999-2025 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=8
 
-inherit toolchain-funcs
+inherit dot-a toolchain-funcs
 
 MY_PV="${PV/_beta/b}"
 
@@ -33,6 +33,8 @@ src_configure() {
 	# make build verbose, bug #429308
 	export V=1
 
+	lto-guarantee-fat
+
 	econf \
 		--disable-pic \
 		--enable-threads \
@@ -48,6 +50,7 @@ src_compile() {
 
 src_install() {
 	default
+	strip-lto-bytecode
 	dodoc Userguide.pdf
 
 	insinto /usr/share/hmmer