This paper is a direct generalization of Baker-Bowler theory to flag matroids, including its moduli interpretation as developed by Baker and the second author for matroids. More explicitly, we extend the notion of flag matroids to flag matroids over any tract, provide cryptomorphic descriptions in terms of basis axioms (Grassmann-Plücker functions), circuit/vector axioms and dual pairs, including additional characterizations in the case of perfect tracts. We establish duality of flag matroids and construct minors. Based on the theory of ordered blue schemes, we introduce flag matroid bundles and construct their moduli space, which leads to algebro-geometric descriptions of duality and minors. Taking rational points recovers flag varieties in several geometric contexts: over (topological) fields, in tropical geometry, and as a generalization of the MacPhersonian.