Yes, this has come before the Court.
Some prominent examples are -
- Mathieu-Mohin and Clerfayt v Belgium (1987), the first time Article 3 was before the European Court of Human Rights, on the complex Belgian system of balancing French-speaking and Dutch-speaking electoral institutions
- Matthews v United Kingdom (1999), on whether people in Gibraltar should be able to vote in elections to the European Parliament
- Hirst v United Kingdom (No 2) (2005), on whether the UK could have a blanket ban on voting applicable to all prisoners
- Riza and others v Bulgaria (2015), on selective interference with the electoral count
In all but the first of these, the Court found a violation of Article 3 of the Protocol. At other times, it has given deference to a State's particular processes, or ruled that a complaint was inadmissible because it did not pertain to the covered type of election.
You may be interested to read the Court's guide to its case-law on the topic (a 34-page PDF) which includes many more citations, and an explanation of the legal reasoning involved.