diff --git a/CHANGELOG.md b/CHANGELOG.md
index 1a482e93..1f5a1910 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,8 +9,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - [#290](https://github.com/nf-core/funcscan/pull/290) Merged pipeline template of nf-core/tools version 2.9, updated references. (by @jfy133)
 
+- [#295](https://github.com/nf-core/funcscan/pull/295) Add Prokka to MultiQC output (by @louperelo)
+
 ### `Fixed`
 
+- [#296](https://github.com/nf-core/funcscan/pull/296) Fixed empty output when saving prodigal annotations. (reported by @louperelo, fix by @jasmezz)
+
 ### `Dependencies`
 
 ### `Deprecated`
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index 88589ded..0c328048 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -15,3 +15,6 @@ export_plots: true
 custom_logo: "nf-core-funcscan_logo_flat_light.png"
 custom_logo_url: https://nf-co.re/funcscan
 custom_logo_title: "nf-core/funcscan"
+
+## Tool specific configuration
+prokka_fn_snames: True
diff --git a/workflows/funcscan.nf b/workflows/funcscan.nf
index ad317a20..17b7e6f8 100644
--- a/workflows/funcscan.nf
+++ b/workflows/funcscan.nf
@@ -282,6 +282,7 @@ workflow FUNCSCAN {
     ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
     ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml'))
     ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect())
+    if(params.annotation_tool=='prokka'){ch_multiqc_files = ch_multiqc_files.mix( PROKKA.out.txt.collect{it[1]}.ifEmpty([])) }
 
     MULTIQC (
         ch_multiqc_files.collect(),