Signs of its tragic destruction can still be clearly seen on the reconstructed Frauenkirche. The dark colour of the old stones and the dimensional differences in the joints between the new and old masonry resemble the scars of healed wounds. They symbolise the message of the reconstructed Frauenkirche, which is closely linked to the church's history. As a place of remembrance the Frauenkirche reminds us of the destruction and suffering that war brings. As a place of hope it reminds us that wounds can heal and that reconciliation is possible.

When archaeologists cleared the rubble, they discovered with amazement and joy that sizeable parts of the altar had remained largely intact: the altar table, the columns with their capitals and parts of the background emerged from the ruins. Some 2,000 separate parts of the ruined altar were salvaged and identified. The different pieces of rubble were painstakingly categorised and included in the archaeological reconstruction. Sketches were made of the pieces found; they were colour tested and categorised by restorers. Almost eighty per cent of the original historical altar was retained. Missing parts were finished off with stone filler. Some were recreated, such as the plaster angel above the praying Jesus, and the halo. When the colours were selected for the altar, care was taken to ensure that the original message was again clear, but that an attentive onlooker could also make out the traces left by the fate this altar shared with the whole church.

The north-western chapel of the lower church shows the clearest signs of the destruction it suffered in the war. Here, the wounds remain unhealed and have been emphasised by the artist Michael Schoenholtz using sculpted elements. A relief-like composition closes off the gap opposite the entrance, leaving a hole in the shape of a cross, as if it has been knocked out. This cross shape appears again, cut into the floor, where it looks like a tomb slab, cut out of the main entity. Finally, it is raised aloft once more in the central part of the church as the cross hanging above the altar.

When the Frauenkirche collapsed on the morning of 15 February 1945 the old church cross fell from a height of some 90 metres or 295 feet, to lie for years under the ruins. The joy and thankfulness were great when, in 1993, archaeologists clearing the rubble managed to salvage it – bent out of shape but not destroyed. It has been put up in the church as a lasting reminder. Visitors to the Frauenkirche are invited to write prayer requests in the book and light a candle next to the cross.