This paper presents an ecotoxicological evaluation of soil fertilized with biogas digestate (BD) or mining waste (MS). The study was performed under pot experiment conditions. BD was added at a dose of 1.5 and 3% to the soil. MS was applied at a dose of 10 and 20%. Samples were collected at the beginning of the experiment and after 180 and 360 days from the start of the study. In addition, a parallel experiment with the addition of CaO was done. This was designed to eliminate the adverse effect of low soil pH on the test organisms. A battery of ecotoxicological tests was used based on tests with plants (Phytotoxkit F), microorganisms (Microtox), and crustaceans (Daphtoxkit F). In most cases, the obtained results showed that the investigated wastes had a stimulating effect on the growth of Lepidium sativum roots. The highest content of BD was an exception since it inhibited the growth of L. sativum roots. After adding BD and MS, both the luminescence of Vibrio fischeri and the mortality of Daphnia magna was at a similar level to that in the control soil. An exception was the significant increase in the mortality of D. magna after 48 h for soil with 3% BD. The tests performed after 6 and 12 months showed that, with time, the toxicity of the waste-amended soil fluctuated, but ultimately decreased in most cases compared to the control. The effect of the addition of CaO on the examined toxicity parameters was different and depended on the experimental variant.