We present a technique of three-dimensional (3-D) differential imaging by the way of incoherent digital holography. We demonstrate that the method is suitable for fluorescence microscopy without the need for unfavorable scanning. We acquire the complex optical field of an incoherent volumetric scene at various times and calculate a complex difference hologram representing only the information, which has changed throughout the volumetric space during the time intervals in-between. We first demonstrate the advanced capability of self-interference incoherent digital holography combined with difference holography to track 3-D changes in a broadband, unfiltered, sunlit scene containing macroscopic continuous objects. This case is particularly remarkable due to the exceptionally short temporal coherence length and excessive build-up of noninterfering source points. We then demonstrate the ease of adaptation to the versatile, functional imaging of fluorescence microscopy.