In some limited areas, namely environmental protection, the EU can force via directives the member states to criminalize certain behaviors:
The contention that criminal law is the exclusive
business of the sovereign state has, however, been challenged by the latest developments in EU law,
both in terms of treaty amendments
and in case law of the Court. In the Environmental Crime Case,
which concerned legislation in the area of environmental policy, the Court held that, under Article 175
EC (now 192 TFEU), the Community had the power to require Member States to enact criminal law
measures if such measures would be ‘essential’ to ensure that the rules on environmental protection
are ‘fully effective’.
from Öberg, J. (2011) "Criminal Sanctions in the Field of EU Environmental Law."
New Journal of European Criminal Law, (4): 402-425
I'm not sure if this has resulted in any individuals (as opposed to companies) being prosecuted under the directive-implementing national laws. The resulting 2008 PECL (Protection of the Environment through Criminal Law) directive has this text:
2008 PECL Directive
The definitive version of the PECL Directive was finally adopted in November 2008 and
Member States are required to bring into force the legislative measures necessary for its
transposition by 26 December 2010.
Offences
Article 3 of the Directive lists and defines common offences and requires that:
Member States shall ensure that the following conduct constitutes a criminal
offence, when unlawful and committed intentionally or with at least serious
negligence:
(a) the discharge, emission or introduction of a quantity of materials or ionising
radiation into air, soil or water, which causes or is likely to cause death or
serious injury to any person or substantial damage to the quality of air, the
quality of soil or the quality of water, or to animals or plants;
(b) the collection, transport, recovery or disposal of waste, including the
supervision of such operations and the aftercare of disposal sites, and
including action taken as a dealer or a broker (waste management), which
causes or is likely to cause death or serious injury to any person or substantial
damage to the quality of air, the quality of soil or the quality of water, or to
animals or plants;
(c) the shipment of waste, where this activity falls within the scope of Article
2(35) of Regulation (EC) No. 1013/2006 …on shipments of waste and is
undertaken in a nonnegligible quantity, whether executed in a single
shipment or in several shipments which appear to be linked;
(d) the operation of a plant in which a dangerous activity is carried out or in
which dangerous substances or preparations are stored or used and which,
outside the plant, causes or is likely to cause death or serious injury to any
person or substantial damage to the quality of air, the quality of soil or the
quality of water, or to animals or plants;
(e) the production, processing, handling, use, holding, storage, transport, import,
export or disposal of nuclear materials or other hazardous radioactive
substances which causes or is likely to cause death or serious injury to any person or substantial damage to the quality of air, the quality of soil or the
quality of water, or to animals or plants;
(f) the killing, destruction, possession or taking of specimens of protected wild
fauna or flora species, except for cases where the conduct concerns a
negligible quantity of such specimens and has a negligible impact on the
conservation status of the species;
(g) trading in specimens of protected wild fauna or flora species or parts or
derivatives thereof, except for cases where the conduct concerns a negligible
quantity of such specimens and has a negligible impact on the conservation
status of the species;
(h) any conduct which causes the significant deterioration of a habitat within a
protected site;
(i) the production, importation, exportation, placing on the market or use of
ozone-depleting substances.
So if poaching protected species somehow was not already a criminal offence in all member countries (or poisoning someone with radioactive materials), that looks like something that could directly affect an individual being criminalized. Most other types of activities criminalized there look like they would mostly apply to companies. In general, the PECL directive was seen as imposing some minimum standards, which are usually exceeded in most member country legislation already.
In theory however, the treaty framework would allow stronger criminal-law environmental protection measures to be pushed through directives; since these normally [meaning if they have the Commision's approval] only require a qualified majority in the Council, they could impose on a country the introduction of criminal sanctions in its national legislation (at least in relation to environmental protection) that a country's legislature [or even its popuplation] doesn't quite approve of.