diff --git a/lib/galaxy/tools/deps/conda_util.py b/lib/galaxy/tools/deps/conda_util.py
index 496828f99af..6632bd0fdd6 100644
--- a/lib/galaxy/tools/deps/conda_util.py
+++ b/lib/galaxy/tools/deps/conda_util.py
@@ -364,6 +364,17 @@ def install_conda(conda_context=None):
             os.remove(script_path)
 
 
+def install_conda_targets(conda_targets, env_name, conda_context=None):
+    conda_context = _ensure_conda_context(conda_context)
+    conda_context.ensure_channels_configured()
+    create_args = [
+        "--name", env_name,  # enviornment for package
+    ]
+    for conda_target in conda_targets:
+        create_args.append(conda_target.package_specifier)
+    return conda_context.exec_create(create_args)
+
+
 def install_conda_target(conda_target, conda_context=None):
     """ Install specified target into a its own environment.
     """
@@ -376,10 +387,14 @@ def install_conda_target(conda_target, conda_context=None):
     return conda_context.exec_create(create_args)
 
 
-def cleanup_failed_install(conda_target, conda_context=None):
+def cleanup_failed_install_of_environment(env, conda_context=None):
     conda_context = _ensure_conda_context(conda_context)
-    if conda_context.has_env(conda_target.install_environment):
-        conda_context.exec_remove([conda_target.install_environment])
+    if conda_context.has_env(env):
+        conda_context.exec_remove([env])
+
+
+def cleanup_failed_install(conda_target, conda_context=None):
+    cleanup_failed_install_of_environment(conda_target.install_environment, conda_context=conda_context)
 
 
 def best_search_result(conda_target, conda_context=None, channels_override=None):
diff --git a/lib/galaxy/tools/deps/resolvers/conda.py b/lib/galaxy/tools/deps/resolvers/conda.py
index f384d1028e4..56e368db41b 100644
--- a/lib/galaxy/tools/deps/resolvers/conda.py
+++ b/lib/galaxy/tools/deps/resolvers/conda.py
@@ -11,10 +11,13 @@ import galaxy.tools.deps.installable
 from ..conda_util import (
     build_isolated_environment,
     cleanup_failed_install,
+    cleanup_failed_install_of_environment,
     CondaContext,
     CondaTarget,
+    hash_conda_packages,
     install_conda,
     install_conda_target,
+    install_conda_targets,
     installed_conda_targets,
     is_conda_target_installed,
     USE_PATH_EXEC_DEFAULT,
@@ -102,6 +105,71 @@ class CondaDependencyResolver(DependencyResolver, ListableDependencyResolver, In
     def clean(self, **kwds):
         return self.conda_context.exec_clean()
 
+    def install_all(self, conda_targets):
+        env = self.merged_environment_name(conda_targets)
+        return_code = install_conda_targets(conda_targets, env, conda_context=self.conda_context)
+        if return_code != 0:
+            is_installed = False
+        else:
+            # Recheck if installed
+            is_installed = self.conda_context.has_env(env)
+
+        if not is_installed:
+            log.debug("Removing failed conda install of {}".format(str(conda_targets)))
+            cleanup_failed_install_of_environment(env, conda_context=self.conda_context)
+
+        return is_installed
+
+    def resolve_all(self, requirements, **kwds):
+        if len(requirements) == 0:
+            return False
+
+        if not os.path.isdir(self.conda_context.conda_prefix):
+            return False
+
+        for requirement in requirements:
+            if requirement.type != "package":
+                return False
+
+        conda_targets = []
+        for requirement in requirements:
+            version = requirement.version
+            if self.versionless:
+                version = None
+
+            conda_targets.append(CondaTarget(requirement.name, version=version))
+
+        preserve_python_environment = kwds.get("preserve_python_environment", False)
+
+        env = self.merged_environment_name(conda_targets)
+        dependencies = []
+
+        is_installed = self.conda_context.has_env(env)
+        if not is_installed and self.auto_install:
+            is_installed = self.install_all(conda_targets)
+
+        if is_installed:
+            for requirement in requirements:
+                dependency = MergedCondaDependency(
+                    self.conda_context,
+                    self.conda_context.env_path(env),
+                    exact=self.versionless or requirement.version is None,
+                    name=requirement.name,
+                    version=requirement.version,
+                    preserve_python_environment=preserve_python_environment,
+                )
+                dependencies.append(dependency)
+
+        return dependencies
+
+    def merged_environment_name(self, conda_targets):
+        if len(conda_targets) > 1:
+            # For continuity with mulled containers this is kind of nice.
+            return "mulled-v1-%s" % hash_conda_packages(conda_targets)
+        else:
+            assert len(conda_targets) == 1
+            return conda_targets[0].install_environment
+
     def resolve(self, name, version, type, **kwds):
         # Check for conda just not being there, this way we can enable
         # conda by default and just do nothing in not configured.
@@ -193,6 +261,48 @@ class CondaDependencyResolver(DependencyResolver, ListableDependencyResolver, In
         return self.conda_context.conda_prefix
 
 
+class MergedCondaDependency(Dependency):
+    dict_collection_visible_keys = Dependency.dict_collection_visible_keys + ['environment_path', 'name', 'version']
+    dependency_type = 'conda'
+
+    def __init__(self, conda_context, environment_path, exact, name=None, version=None, preserve_python_environment=False):
+        self.activate = conda_context.activate
+        self.conda_context = conda_context
+        self.environment_path = environment_path
+        self._exact = exact
+        self._name = name
+        self._version = version
+        self.cache_path = None
+        self._preserve_python_environment = preserve_python_environment
+
+    @property
+    def exact(self):
+        return self._exact
+
+    @property
+    def name(self):
+        return self._name
+
+    @property
+    def version(self):
+        return self._version
+
+    def shell_commands(self, requirement):
+        if self._preserve_python_environment:
+            # On explicit testing the only such requirement I am aware of is samtools - and it seems to work
+            # fine with just appending the PATH as done below. Other tools may require additional
+            # variables in the future.
+            return """export PATH=$PATH:'%s/bin' """ % (
+                self.environment_path,
+            )
+        else:
+            return """[ "$CONDA_DEFAULT_ENV" = "%s" ] || . %s '%s' > conda_activate.log 2>&1 """ % (
+                self.environment_path,
+                self.activate,
+                self.environment_path
+            )
+
+
 class CondaDependency(Dependency):
     dict_collection_visible_keys = Dependency.dict_collection_visible_keys + ['environment_path', 'name', 'version']
     dependency_type = 'conda'
diff --git a/test/functional/tools/mulled_example_conflict.xml b/test/functional/tools/mulled_example_conflict.xml
new file mode 100644
index 00000000000..4df76c2fab1
--- /dev/null
+++ b/test/functional/tools/mulled_example_conflict.xml
@@ -0,0 +1,17 @@
+<tool id="mulled_example_conflict" name="mulled_example_conflict" version="0.1.0">
+    <!-- Tool can't be resolved with older style Conda resolution - all requirements
+         must be installed together to ensure there is no conflict. -->
+    <command detect_errors="exit_code"><![CDATA[
+        lumpy 2>&1 | grep -q structural
+    ]]></command>
+    <requirements>
+        <requirement type="package" version="0.2.12">lumpy-sv</requirement>
+        <requirement type="package" version="1.11.2">numpy</requirement>
+    </requirements>
+    <inputs>
+        <param name="input1" type="text" value="The value" />
+    </inputs>
+    <outputs>
+        <data name="out_file1" format="txt" />
+    </outputs>
+</tool>
diff --git a/test/functional/tools/samples_tool_conf.xml b/test/functional/tools/samples_tool_conf.xml
index 58ecb3b6f5a..ab7ed822054 100644
--- a/test/functional/tools/samples_tool_conf.xml
+++ b/test/functional/tools/samples_tool_conf.xml
@@ -123,6 +123,7 @@
   </section>
 
   <tool file="mulled_example_multi_1.xml" />
+  <tool file="mulled_example_conflict.xml" />
 
   <tool file="simple_constructs.yml" />