diff --git a/CHANGELOG.md b/CHANGELOG.md
index 7414f250..c3a338b6 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,6 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Added`
 
+- [#700](https://github.com/nf-core/ampliseq/pull/700) - Optional `--save_intermediates` to publish QIIME2 data objects (.qza) and visualisation objects (.qzv)
+
 ### `Changed`
 
 ### `Fixed`
diff --git a/conf/modules.config b/conf/modules.config
index 7b28c7e9..b159d8d0 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -664,10 +664,10 @@ process {
 
     withName: 'QIIME2_INASV_BPAVG' {
         publishDir = [
-            path: { "${params.outdir}/qiime2/input" },
+            path: { "${params.outdir}/qiime2/barplot_average" },
             mode: params.publish_dir_mode,
             pattern: "*.qza",
-            enabled: false
+            enabled: params.save_intermediates
         ]
     }
 
@@ -758,25 +758,55 @@ process {
 
     withName: QIIME2_ALPHARAREFACTION {
         publishDir = [
-            path: { "${params.outdir}/qiime2" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            [
+                path: { "${params.outdir}/qiime2" },
+                mode: params.publish_dir_mode,
+                saveAs: { filename -> filename.equals('versions.yml') || filename.endsWith('.qzv') ? null : filename }
+            ],
+            [
+                path: { "${params.outdir}/qiime2/alpha-rarefaction" },
+                mode: params.publish_dir_mode,
+                pattern: "*.qzv",
+                enabled: params.save_intermediates
+            ]
         ]
     }
 
     withName: 'QIIME2_DIVERSITY_CORE|QIIME2_DIVERSITY_ALPHA|QIIME2_DIVERSITY_BETA|QIIME2_DIVERSITY_BETAORD' {
         publishDir = [
-            path: { "${params.outdir}/qiime2/diversity" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') || filename.endsWith('.qza') ? null : filename }
+            [
+                path: { "${params.outdir}/qiime2/diversity" },
+                mode: params.publish_dir_mode,
+                saveAs: { filename -> filename.equals('versions.yml') || filename.endsWith('.qza') || filename.endsWith('.qzv') ? null : filename }
+            ],
+            [
+                path: { "${params.outdir}/qiime2/diversity/qza_qzv" },
+                mode: params.publish_dir_mode,
+                pattern: "*{.qza,.qzv}",
+                enabled: params.save_intermediates
+            ],
+            [
+                path: { "${params.outdir}/qiime2/diversity/qza_qzv" },
+                mode: params.publish_dir_mode,
+                saveAs: { filename -> filename.endsWith('.qza') ? filename : null },
+                enabled: params.save_intermediates
+            ]
         ]
     }
 
     withName: QIIME2_DIVERSITY_ADONIS {
         publishDir = [
-            path: { "${params.outdir}/qiime2/diversity/beta_diversity" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            [
+                path: { "${params.outdir}/qiime2/diversity/beta_diversity" },
+                mode: params.publish_dir_mode,
+                saveAs: { filename -> filename.equals('versions.yml') || filename.endsWith('.qzv') ? null : filename }
+            ],
+            [
+                path: { "${params.outdir}/qiime2/diversity/beta_diversity/adonis" },
+                mode: params.publish_dir_mode,
+                pattern: "*.qzv",
+                enabled: params.save_intermediates
+            ]
         ]
     }
 
diff --git a/modules/local/qiime2_alphararefaction.nf b/modules/local/qiime2_alphararefaction.nf
index 23dfe602..d5313174 100644
--- a/modules/local/qiime2_alphararefaction.nf
+++ b/modules/local/qiime2_alphararefaction.nf
@@ -11,6 +11,7 @@ process QIIME2_ALPHARAREFACTION {
 
     output:
     path("alpha-rarefaction/*"), emit: rarefaction
+    path("*.qzv")              , emit: qzv
     path "versions.yml"        , emit: versions
 
     when:
diff --git a/modules/local/qiime2_diversity_adonis.nf b/modules/local/qiime2_diversity_adonis.nf
index 0672aa4f..946a0512 100644
--- a/modules/local/qiime2_diversity_adonis.nf
+++ b/modules/local/qiime2_diversity_adonis.nf
@@ -9,6 +9,7 @@ process QIIME2_DIVERSITY_ADONIS {
 
     output:
     path("adonis/*")     , emit: html
+    path("*.qzv")        , emit: qzv
     path "versions.yml"  , emit: versions
 
     when:
diff --git a/modules/local/qiime2_diversity_alpha.nf b/modules/local/qiime2_diversity_alpha.nf
index 743ed518..ba755d51 100644
--- a/modules/local/qiime2_diversity_alpha.nf
+++ b/modules/local/qiime2_diversity_alpha.nf
@@ -9,6 +9,7 @@ process QIIME2_DIVERSITY_ALPHA {
 
     output:
     path("alpha_diversity/*"), emit: alpha
+    path("*.qzv")            , emit: qzv
     path "versions.yml"      , emit: versions
 
     when:
diff --git a/modules/local/qiime2_diversity_beta.nf b/modules/local/qiime2_diversity_beta.nf
index c48b6b4c..eef3cdf2 100644
--- a/modules/local/qiime2_diversity_beta.nf
+++ b/modules/local/qiime2_diversity_beta.nf
@@ -9,6 +9,7 @@ process QIIME2_DIVERSITY_BETA {
 
     output:
     path("beta_diversity/*"), emit: beta
+    path("*.qzv")           , emit: qzv
     path "versions.yml"     , emit: versions
 
     when:
diff --git a/modules/local/qiime2_diversity_betaord.nf b/modules/local/qiime2_diversity_betaord.nf
index 658cf765..9e54b544 100644
--- a/modules/local/qiime2_diversity_betaord.nf
+++ b/modules/local/qiime2_diversity_betaord.nf
@@ -9,6 +9,7 @@ process QIIME2_DIVERSITY_BETAORD {
 
     output:
     path("beta_diversity/*"), emit: beta
+    path("*.qzv")           , emit: qzv
     path "versions.yml"     , emit: versions
 
     when:
diff --git a/nextflow.config b/nextflow.config
index b65af8c8..84a11fc6 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -22,6 +22,7 @@ params {
     metadata                   = null
 
     // Other options
+    save_intermediates= false
     trunc_qmin        = 25
     trunc_rmin        = 0.75
     trunclenf         = null
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 938690d4..84e95739 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -57,6 +57,12 @@
                     "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
                     "fa_icon": "fas fa-folder-open"
                 },
+                "save_intermediates": {
+                    "type": "boolean",
+                    "default": 100,
+                    "description": "Save intermediate results such as QIIME2's qza and qzv files",
+                    "fa_icon": "fas fa-folder-open"
+                },
                 "email": {
                     "type": "string",
                     "description": "Email address for completion summary.",