West Midlands Police charged 34-year-old Carl Stephens, of The Radleys, Marston Green, in Birmingham, with causing religiously aggravated harassment, alarm and distress.
He will appear at Birmingham Magistrates' Court after police arrested him in the early hours of Wednesday (10 June). The animals' remains were found on the grounds of the Hermitage Road premises on 12 April.
An investigation was launched by Solihull Council after claims the facility was being used as a mosque and was in breach of planning consent.
More than 3,000 people signed an online petition against its use for worship. Chief superintendent Alex Murray said: "Solihull has a hard-earned reputation as a place where people from different backgrounds have really strong bonds.
"It is an area where communities are respectful and considerate of one another and when that harmony is disrupted by the actions of an ignorant minority, people should rest assured we will take action to ensure justice is served.
"In this case, a huge amount of effort has been involved in trying to find the arrested man, with addresses being tried again and again without let up.
"There will be no tolerance of any type of hate crime here in Solihull and we will do all we can to trace anyone we suspect of being involved in it."
International Business Times