diff --git a/biology/migrate/Makefile b/biology/migrate/Makefile
index c524444a06bf..fc3734ae592f 100644
--- a/biology/migrate/Makefile
+++ b/biology/migrate/Makefile
@@ -1,60 +1,64 @@
 PORTNAME=	migrate
-DISTVERSION=	5.0.5
+DISTVERSION=	5.0.6
 CATEGORIES=	biology
 MASTER_SITES=	https://peterbeerli.com/migrate-html5/download_version4/
 DISTNAME=	${PORTNAME}-${PORTVERSION}.src
 
 MAINTAINER=	eduardo@FreeBSD.org
 COMMENT=	Program to estimate population sizes and migration rates
 WWW=		https://popgen.sc.fsu.edu/Migrate/Migrate-n.html
 
 LICENSE=	MIT
 LICENSE_FILE=	${WRKSRC}/../README
 
 # Waiting on build reports, 2024-03-27
 #BROKEN_armv6=	fails to build: make[2]: cannot open makefile
 #BROKEN_armv7=	fails to build: make[2]: cannot open makefile
 #BROKEN_mips=	fails to build: make[2]: cannot open makefile
 #BROKEN_riscv64=	fails to build: make[2]: cannot open makefile
 
 GNU_CONFIGURE=	yes
 CONFIGURE_ENV=	ac_cv_prog_GMAKE="${MAKE}"
 MAKE_ARGS=	PRETTYCFLAGS="${CFLAGS} -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++"
 
 CONFLICTS_INSTALL=	py*-sqlalchemy-migrate # bin/migrate
 
 EXTRACT_AFTER_ARGS=	--no-same-owner --no-same-permissions --exclude zlib
 WRKSRC=		${WRKDIR}/${PORTNAME}-${PORTVERSION}/src
 
 PORTDOCS=	${PORTNAME}.html HISTORY README README_PARALLEL_GENERAL
 PORTEXAMPLES=	*
 
 OPTIONS_DEFINE=		DOCS EXAMPLES THREAD
 THREAD_DESC=		Build with THREAD support
 THREAD_ALL_TARGET=	thread
 
+# Upstream tarball contains objects and binaries that need to be clean
+post-extract:
+	cd ${WRKSRC} && ${RM} -f *.o haru/*.o migrate-n migrate-n-mpi
+
 post-patch:
 	@${REINPLACE_CMD} -e 's|="-O "|="$$CFLAGS"|g' ${WRKSRC}/configure
 	@${REINPLACE_CMD} -e '/PRETTY$$/d' ${WRKSRC}/src/definitions.h
 	@${REINPLACE_CMD} -e 's|-O3||g' ${WRKSRC}/haru/makefile.gcc
 
 do-install:
 	${INSTALL_PROGRAM} ${WRKSRC}/${PORTNAME}-n ${STAGEDIR}${PREFIX}/bin
 	${LN} -sf ${PORTNAME}-n ${STAGEDIR}${PREFIX}/bin/${PORTNAME}
 	${INSTALL_MAN} ${WRKSRC}/${PORTNAME}.1 \
 		${STAGEDIR}${PREFIX}/share/man/man1
 	${LN} -sf ${PORTNAME}.1 \
 		${STAGEDIR}${PREFIX}/share/man/man1/${PORTNAME}-n.1
 
 do-install-DOCS-on:
 	@${MKDIR} ${STAGEDIR}${DOCSDIR}
 	${INSTALL_DATA} ${PORTDOCS:S,^,${WRKSRC}/../,} ${STAGEDIR}${DOCSDIR}
 	@${MKDIR} ${STAGEDIR}${DOCSDIR}/graphics
 	${INSTALL_DATA} ${WRKSRC}/../graphics/* ${STAGEDIR}${DOCSDIR}/graphics
 
 do-install-EXAMPLES-on:
 	@${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
 	${INSTALL_DATA} ${WRKSRC}/../example/[A-Za-z]* \
 		${STAGEDIR}${EXAMPLESDIR}
 
 .include <bsd.port.mk>
diff --git a/biology/migrate/distinfo b/biology/migrate/distinfo
index 498a5f72dd3d..927666e293df 100644
--- a/biology/migrate/distinfo
+++ b/biology/migrate/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1711535851
-SHA256 (migrate-5.0.5.src.tar.gz) = 43d456f2432c0ec77ad33877f184d3b4b36f61e416f8fffa51077768df91ea51
-SIZE (migrate-5.0.5.src.tar.gz) = 4746835
+TIMESTAMP = 1711916315
+SHA256 (migrate-5.0.6.src.tar.gz) = 9772ae5bdc5be81af6830a9240aa5a0f90ae9fb52d70e46cf4f50a8b389f8925
+SIZE (migrate-5.0.6.src.tar.gz) = 8254038