Going up against large organisations such as Warner Brothers, Diageo and Nationwide, it picked up five prizes including best app, best website and best use of social media.
It comes after the Church made a big investment into its work online.
Based out of Church House, the digital team oversees the Church's presence online and uses Christian festivals to reach out to the country.
Speaking to Premier, the Church of England's head of digital, Adrian Harris said: "We're absolutely thrilled to have won five awards.
"They recognise the passion and hard work of many colleagues across the Church over the last two years.
"It's wonderful to see the way that dioceses and local churches are engaging in digital for the opportunities it brings to grow people's faith, bring people to faith and encourage church attendance."
Announcing the Church as the 'best in-house digital team of the year', organisers said: "The Church has been recognised for its efforts over the past few years in building a digital function where once there was none.
"The church is now digitally savvy and explores new technologies - like Amazon's Alexa voice assistant - with ease."
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