MK Dons were the visitors to the club's training base at Carton House and provided stiff opposition on a hot day.
Former England striker Alan Smith handed the visitors the lead in the 28th minute before Koby Arthur levelled scores with a fine effort six minutes later.
Shaun Williams converted from the spot shortly after the interval before George Baldock and Daniel Powell wrapped up the win for MK Dons.
Apart from Tom Adeyemi, Matt Green and Neal Eardley, who were rested as a precaution, every member of Lee Clark's squad was involved, with Darren Randolph the only unused sub.
The opening quarter-of-an-hour offered little goalscoring opportunities for either side but it was Blues who had the first real chance in the 23rd minute.
Darren Ambrose's fine cross from the right fell to Shinnie, whose shot was deflected into the path of trialist Liam Davis only for Tom Flanagan to block on the line.
Smith fired Karl Robinson's side into the lead with the half-an-hour approaching. The lone forward wriggled into space in the area before cracking a shot in off the underside of the crossbar.
However, Arthur struck back with a fine move that he started. After stealing possession off Dean Lewington, the Ghanaian played a one-two with Lee Novak on the left before curling an effort into the far corner, leaving 'keeper David Martin stunned.
Novak himself had the ball in the net moments after when he bundled home Wade Elliott's cross but the effort was ruled out for offside.
Chris Burke and Olly Lee were introduced to the action at the break, for Arthur and Ambrose respectively. Burke's cross from the right was cleared to Callum Reilly in the 52nd minute but Martin got a hold of his low strike from 20 yards.
Dan Burn was adjudged to have fouled MK Dons sub Izale McLeod in the area moments later and Williams stepped up to fire an inch-perfect penalty beyond the reach of Colin Doyle.
Four changes on the hour mark, with Paul Robinson, Hayden Mullins, Jonathan Spector and Nikola Zigic introduced, knocked Blues' rhythm and MK Dons immediately took advantage; Powell rifling home a volley from the edge of the box.
Baldock added a fourth in the 70th minute having cut in from the right before firing home a low, left-footed shot.
Shinnie tested Martin with a free-kick at one end before Doyle did well to deny Dele Alli at the other by diverted the forward's shot on to the roof of his net.
Blues: Colin Doyle; Wade Elliott (Jonathan Spector 60), Kyle Bartley (Hayden Mullins 60), Mitch Hancox, Dan Burn (Paul Robinson 60), Liam Davis; Callum Reilly, Darren Ambrose (Olly Lee H/T); Koby Arthur (Chris Burke H/T); Lee Novak (Nikola Zigic 60), Andrew Shinnie. Unused sub: Darren Randolph.
MK Dons: David Martin, Tom Flanagan, Anthony Kay, Shaun Williams (George Baldock 60), Dean Lewington, Stephen Gleeson (Brendan Galloway 64), Daniel Powell, Giorgio Rosulo (Izale McLeod H/T), Dele Alli (Rosulo 83), Alan Smith (Santiago Aloi H/T), Darren Potter.