diff --git a/modules/local/colabfold_batch/Dockerfile b/modules/local/colabfold_batch/Dockerfile
index d886bfc7..264a5a7b 100644
--- a/modules/local/colabfold_batch/Dockerfile
+++ b/modules/local/colabfold_batch/Dockerfile
@@ -7,7 +7,7 @@ ARG CUDA_VERSION
 
 LABEL org.opencontainers.image.title="nf-core/proteinfold_colabfold" \
     org.opencontainers.image.description="Docker image containing all software requirements to run the COLABFOLD_BATCH module using the nf-core/proteinfold pipeline" \
-    org.opencontainers.image.version="2.0.0" \
+    org.opencontainers.image.version="2.1.0" \
     org.opencontainers.image.authors="Joshua Storm Caley <j.caley@unsw.edu.au>" \
     org.opencontainers.image.source="https://github.com/nf-core/proteinfold" \
     org.opencontainers.image.licenses="MIT"
@@ -25,10 +25,10 @@ RUN apt-get update && \
     CONDA_OVERRIDE_CUDA=$(echo $CUDA_VERSION | cut -d'.' -f1,2) mamba install -c conda-forge -c nvidia -c bioconda \
         openmm pdbfixer kalign2=2.04 hhsuite=3.3.0 -y && \
     \
-    pip install --no-cache-dir --no-warn-conflicts "colabfold[alphafold-minus-jax] @ git+https://github.com/sokrypton/ColabFold.git@e8ebd9a" && \
+    pip install --no-cache-dir --no-warn-conflicts "colabfold[alphafold-minus-jax] @ git+https://github.com/sokrypton/ColabFold.git@v1.6.2" && \
     pip install --no-cache-dir silence_tensorflow && \
     pip uninstall -y jax jaxlib || true && \
-    pip install --no-cache-dir "jax[cuda12]==0.5.3" "jaxlib==0.5.3" && \
+    pip install --no-cache-dir "jax[cuda12]==0.6.2" && \
     \
     mamba clean -a -y && \
     rm -rf /usr/local/pkgs && \
diff --git a/modules/local/mmseqs_colabfoldsearch/Dockerfile b/modules/local/mmseqs_colabfoldsearch/Dockerfile
index 9cf1d490..bd07d4d7 100644
--- a/modules/local/mmseqs_colabfoldsearch/Dockerfile
+++ b/modules/local/mmseqs_colabfoldsearch/Dockerfile
@@ -1,5 +1,28 @@
+ARG COLABFOLD_REF=c35de0221f4d297a39edf4cf292ba2832e321edc
+ARG MMSEQS2_REPOSITORY=https://github.com/jscgh/MMseqs2.git
+ARG MMSEQS2_REF=c0434b5a5951987fa025d279af64b298d20f27ff
+
+FROM --platform=linux/amd64 ghcr.io/steineggerlab/build-containers:main-x86_64 AS mmseqs-builder
+
+ARG MMSEQS2_REPOSITORY
+ARG MMSEQS2_REF
+
+WORKDIR /opt/mmseqs2
+
+RUN git init . && \
+    git remote add origin "${MMSEQS2_REPOSITORY}" && \
+    git fetch --depth 1 origin "${MMSEQS2_REF}" && \
+    git checkout --detach FETCH_HEAD && \
+    cmake -S . -B build -GNinja \
+        -DCMAKE_BUILD_TYPE=Release \
+        -DHAVE_TESTS=0 \
+        -DHAVE_SSE4_1=1 \
+        -DFORCE_STATIC_DEPS=1 && \
+    cmake --build build -j"$(nproc)"
+
 FROM ubuntu:24.04
-ARG MMSEQS2_VERSION=18-8cc5c
+
+ARG COLABFOLD_REF
 
 LABEL org.opencontainers.image.title="nf-core/proteinfold_mmseqs_colabfoldsearch" \
     org.opencontainers.image.description="Lightweight Docker image containing all software requirements to run the MMSEQS_COLABFOLDSEARCH module using the nf-core/proteinfold pipeline" \
@@ -13,23 +36,16 @@ RUN apt-get update && \
         python3 \
         python3-dev \
         python3-pip \
-        wget \
         git \
         build-essential \
         cmake && \
     ln -sf /usr/bin/python3 /usr/bin/python && \
     \
     pip install --no-cache-dir --break-system-packages \
-        "colabfold @ git+https://github.com/sokrypton/ColabFold.git@v1.6.1" && \
-    \
-    wget -q https://github.com/soedinglab/MMseqs2/releases/download/${MMSEQS2_VERSION}/mmseqs-linux-sse41.tar.gz && \
-    tar xzf mmseqs-linux-sse41.tar.gz && \
-    cp mmseqs/bin/* /usr/local/bin/ && \
-    rm -rf mmseqs mmseqs-linux-sse41.tar.gz && \
+        "colabfold @ git+https://github.com/sokrypton/ColabFold.git@${COLABFOLD_REF}" && \
     \
     apt-get remove -y \
         python3-dev \
-        wget \
         git \
         build-essential \
         cmake && \
@@ -38,6 +54,10 @@ RUN apt-get update && \
     rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* && \
     pip cache purge
 
+COPY --from=mmseqs-builder /opt/mmseqs2/build/src/mmseqs /usr/local/bin/mmseqs
+
+RUN mmseqs version
+
 ENV MPLBACKEND=Agg
 ENV MPLCONFIGDIR=/tmp/mplconfig
 ENV XDG_CACHE_HOME=/tmp/xdg_cache