Natural compounds such as plant secondary metabolites (PSM) can be used to replace antibiotic growth promoters as rumen modifiers. In this study, the effectiveness of stored and freshly extracted Aloe vera (AV), Azadirachta indica (AZ), Moringa oleifera (MO), Jatropha curcas (JA), Tithonia diversifolia (TD) and Carica papaya (CP) crude extract and monensin on in vitro gas and methane production, organic matter digestibility (IVOMD) and volatile fatty acids (VFA) were evaluated using a total mixed ration (TMR), lucerne or Eragrostis curvula substrates. Fresh extracts were processed from the same batch of frozen (−20 °C) plant material a few days before the trial while the stored extracts were extracted and stored at 4 °C for 12 months prior to the study. Extraction was done by solubilising 50 g freeze-dried plant material in 500 mL 100% methanol. Four mL of reconstituted 50 mg crude extract per 1000 mL distilled water was added per incubation vial, which already contained 400 mg substrate and in vitro fermentation, and gas production and IVOMD evaluation were carried out using standard procedures. Results showed that storing plant extracts for 12 months did not affect the activity or stability of metabolites present in the crude extracts, as shown by the lack of differences in total gas production (TGP) and methane produced between fresh or stored extracts across the substrates. In the TMR substrate, plant extracts increased IVOMD but did not affect TGP and methane production, whereas monensin did not have any effect. Plant extracts increased IVOMD of Eragrostis substrate and supressed methane production to a greater extent than monensin (p < 0.05). It can be concluded that storing plant extracts for up to 12 months did not compromise their efficacy. In addition, the use of 50 mg/kg of AV, AZ, MO, JA, TD and CP extract to a forage-based diet will reduce methane production while improving feed digestibility.