diff --git a/modules/nf-core/mmseqs/makepaddedseqdb/environment.yml b/modules/nf-core/mmseqs/makepaddedseqdb/environment.yml
new file mode 100644
index 000000000000..072223f2aace
--- /dev/null
+++ b/modules/nf-core/mmseqs/makepaddedseqdb/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::mmseqs2=18.8cc5c
diff --git a/modules/nf-core/mmseqs/makepaddedseqdb/main.nf b/modules/nf-core/mmseqs/makepaddedseqdb/main.nf
new file mode 100644
index 000000000000..61857c179f67
--- /dev/null
+++ b/modules/nf-core/mmseqs/makepaddedseqdb/main.nf
@@ -0,0 +1,51 @@
+process MMSEQS_MAKEPADDEDSEQDB {
+    tag "${meta.id}"
+    label 'process_low'
+    conda "${moduleDir}/environment.yml"
+
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/fe/fe49c17754753d6cd9a31e5894117edaf1c81e3d6053a12bf6dc8f3af1dffe23/data'
+        : 'community.wave.seqera.io/library/mmseqs2:18.8cc5c--af05c9a98d9f6139'}"
+
+    input:
+    tuple val(meta), path(db_in)
+
+    output:
+    tuple val(meta), path("${prefix}/"), emit: db_padded
+    tuple val("${task.process}"), val('mmseqs'), eval('mmseqs version'), topic: versions, emit: versions_mmseqs
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def args2 = task.ext.args2 ?: '*.dbtype'
+    prefix = task.ext.prefix ?: "${meta.id}"
+    if ("${db_in}" == "${prefix}") {
+        error("Input and output names of databases are the same, set prefix in module configuration to disambiguate!")
+    }
+    """
+    DB_TARGET_PATH_NAME=\$(find -L "${db_in}/" -maxdepth 1 -name "${args2}" | sed 's/\\.[^.]*\$//' | sed -e 'N;s/^\\(.*\\).*\\n\\1.*\$/\\1\\n\\1/;D' )
+    mkdir -p ${prefix}
+    mmseqs \\
+        makepaddedseqdb \\
+        \$DB_TARGET_PATH_NAME \\
+        ${prefix}/${prefix} \\
+        ${args}
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    echo ${args}
+    mkdir -p ${prefix}
+    touch ${prefix}/${prefix}
+    touch ${prefix}/${prefix}.dbtype
+    touch ${prefix}/${prefix}.index
+    touch ${prefix}/${prefix}.lookup
+    touch ${prefix}/${prefix}_h
+    touch ${prefix}/${prefix}_h.dbtype
+    touch ${prefix}/${prefix}_h.index
+    """
+}
diff --git a/modules/nf-core/mmseqs/makepaddedseqdb/meta.yml b/modules/nf-core/mmseqs/makepaddedseqdb/meta.yml
new file mode 100644
index 000000000000..8858d9bb9908
--- /dev/null
+++ b/modules/nf-core/mmseqs/makepaddedseqdb/meta.yml
@@ -0,0 +1,64 @@
+name: "mmseqs_makepaddedseqdb"
+description: Create an MMseqs padded database from an existing MMseqs database
+keywords:
+  - protein sequence
+  - databases
+  - clustering
+  - searching
+  - indexing
+  - mmseqs2
+tools:
+  - "mmseqs":
+      description: "MMseqs2: ultra fast and sensitive sequence search and clustering
+        suite"
+      homepage: "https://github.com/soedinglab/MMseqs2"
+      documentation: "https://mmseqs.com/latest/userguide.pdf"
+      tool_dev_url: "https://github.com/soedinglab/MMseqs2"
+      doi: "10.1093/bioinformatics/btw006"
+      licence:
+        - "GPL v3"
+      identifier: biotools:mmseqs
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'test', single_end:false ]`
+    - db_in:
+        type: directory
+        description: Input of existing MMseqs database
+output:
+  db_padded:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'test', single_end:false ]`
+      - "${prefix}/":
+          type: directory
+          description: The padded MMseqs2 database
+  versions_mmseqs:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - mmseqs:
+          type: string
+          description: The name of the tool
+      - mmseqs version:
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - mmseqs:
+          type: string
+          description: The name of the tool
+      - mmseqs version:
+          type: eval
+          description: The expression to obtain the version of the tool
+authors:
+  - "@nbtm-sh"
+maintainers:
+  - "@nbtm-sh"
diff --git a/modules/nf-core/mmseqs/makepaddedseqdb/tests/main.nf.test b/modules/nf-core/mmseqs/makepaddedseqdb/tests/main.nf.test
new file mode 100644
index 000000000000..6c3ae4b7ea60
--- /dev/null
+++ b/modules/nf-core/mmseqs/makepaddedseqdb/tests/main.nf.test
@@ -0,0 +1,49 @@
+nextflow_process {
+
+    name "Test Process MMSEQS_MAKEPADDEDSEQDB"
+    script "../main.nf"
+    process "MMSEQS_MAKEPADDEDSEQDB"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "mmseqs"
+    tag "mmseqs/makepaddedseqdb"
+    tag "mmseqs/createdb"
+
+    config "./nextflow.config"
+
+    setup {
+        run("MMSEQS_CREATEDB") {
+            script "../../../mmseqs/createdb/main.nf"
+            process {
+                """
+                input[0] = [ [ id:'test_query' ],
+                file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true)
+                ]
+                """
+            }
+        }
+    }
+
+    test("mmseqs_db sarscov2 contigs") {
+
+        when {
+            params {
+                module_prefix = "test_query_gpu"
+            }
+            process {
+                """
+                input[0] = MMSEQS_CREATEDB.out.db
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(sanitizeOutput(process.out)).match()
+                }
+            )
+        }
+
+    }
+}
diff --git a/modules/nf-core/mmseqs/makepaddedseqdb/tests/main.nf.test.snap b/modules/nf-core/mmseqs/makepaddedseqdb/tests/main.nf.test.snap
new file mode 100644
index 000000000000..8ce6f93de878
--- /dev/null
+++ b/modules/nf-core/mmseqs/makepaddedseqdb/tests/main.nf.test.snap
@@ -0,0 +1,36 @@
+{
+    "mmseqs_db sarscov2 contigs": {
+        "content": [
+            {
+                "db_padded": [
+                    [
+                        {
+                            "id": "test_query"
+                        },
+                        [
+                            "test_query_gpu:md5,5b24585ba92fd826c78b8664c63b4e95",
+                            "test_query_gpu.dbtype:md5,01d39098f2bfee5c808a3b4ff54deac2",
+                            "test_query_gpu.index:md5,5946b4989d08320d9daca503155ba693",
+                            "test_query_gpu.lookup:md5,3eb85c645034a0717db62ef0a3da5479",
+                            "test_query_gpu_h:md5,a9fca4931be476b8f302cc27b5dff9b0",
+                            "test_query_gpu_h.dbtype:md5,740bab4f9ec8808aedb68d6b1281aeb2",
+                            "test_query_gpu_h.index:md5,ce0ca30c2e57677077cc23823ef17206"
+                        ]
+                    ]
+                ],
+                "versions_mmseqs": [
+                    [
+                        "MMSEQS_MAKEPADDEDSEQDB",
+                        "mmseqs",
+                        "18.8cc5c"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-02-25T10:33:19.910807101",
+        "meta": {
+            "nf-test": "0.9.4",
+            "nextflow": "25.04.6"
+        }
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/mmseqs/makepaddedseqdb/tests/nextflow.config b/modules/nf-core/mmseqs/makepaddedseqdb/tests/nextflow.config
new file mode 100644
index 000000000000..735a3eb0904f
--- /dev/null
+++ b/modules/nf-core/mmseqs/makepaddedseqdb/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: "MMSEQS_MAKEPADDEDSEQDB" {
+        ext.prefix = params.module_prefix
+    }
+}