[9] Beginning September 17, 2007, with the Raleigh Boot Camp, Acts 29 began using Great Commission Ministries as its mission agency for fundraising and leadership training.

[21][22] However, Darrin Patrick, former vice president of Acts 29 has pointed out "bad things" in the emerging church such as "the fascination with deconstructing almost everything while building almost nothing", and "ugly things" such as "conversing about God's Word [the Bible] to the neglect of obeying it, deviating from historical orthodoxy and the lack of clarity regarding issues of theology and sexuality.

[25][26] Christian Piatt of the Huffington Post has criticized the network for disguising the traditional evangelical agenda of conformity and conversion behind the veneer of the new missional church movement.

[28] In February 2020, it was announced that Steve Timmis had been removed from the position of CEO of the Acts 29 Network amid allegations of an abusive leadership style; five staff members had previously raised similar concerns with Chandler in 2015, only to be fired and asked to sign non-disclosure agreements.

The Village Church in Dallas offered a general apology after a female member was disciplined for annulling her marriage to a man who admitted to viewing child pornography.