Recording of transient absorption microscopy images requires fast detection of minute optical density changes, which is typically achieved with high-repetition-rate laser sources and lock-in detection. Here, we present a highly flexible and cost-efficient detection scheme based on a conventional photodiode and an USB oscilloscope with MHz bandwidth, that deviates from the commonly used lock-in setup and achieves benchmark sensitivity. Our scheme combines shot-to-shot evaluation of pump-probe and probe-only measurements, a home-built photodetector circuit optimized for low pulse energies applying low-pass amplification, and a custom evaluation algorithm based on Fourier transformation. Advantages of this approach include abilities to simultaneously monitor multiple pulse modulation frequencies, implement the detection of additional pulse sequences (e.g., pump-only), and expand to multiple parallel detection channels for wavelength-dispersive probing. With a 40 kHz repetition-rate laser system powering two non-collinear optical parametric amplifiers for wide tuneability, we find that laser pulse fluctuations limit the sensitivity of the setup, while the detection scheme has negligible contribution. We demonstrate the 2-D imaging performance of our transient absorption microscope with studies on micro-crystalline molecular thin films.