High-dimensional (HD) entanglement promises both enhanced key rates and overcoming obstacles faced by modern-day quantum communication. However, modern convex optimization-based security arguments are limited by computational constraints; thus, accessible dimensions are far exceeded by progress in HD photonics, bringing forth a need for efficient methods to compute key rates for large encoding dimensions. In response to this problem, we present a flexible analytic framework facilitated by the dual of a semi-definite program and diagonalizing operators inspired by entanglement-witness theory, enabling the efficient computation of key rates in high-dimensional systems. To facilitate the latter, we show how matrix completion techniques can be incorporated to effectively yield improved, computable bounds on the key rate in paradigmatic high-dimensional systems of time- or frequency-bin entangled photons and beyond.