Students’ habits of mind (HoM) and disorienting dilemmas (DD) are challenging to investigate and have rarely been explored. Yet, in the past Covid-19 pandemic, students faced many academic and non-academic problems. For example, in Indonesia, 89 million parents lost their jobs, which influenced students’ emotions in their learning process. This paper applied explanatory mixed methods to address students’ HoM and DD in agriculture colleges in Yogyakarta, Indonesia. Two hundred and eleven students voluntarily participated in the online closed- and open-ended survey responses. The first quantitative data were analyzed using the Rasch model of application while Nvivo12 was used for the analysis of the latter. The quantitative data were focused on how agricultural English students perceived HoM; meanwhile, the qualitative data explored a catalyst and a life crisis under the students’ DD. Then, the two research questions were comparatively discussed: (1) How do Agricultural students perceive their HoM and DD during learning English; and (2) What factors influence them in learning English? As illustrated in the Rasch map, the result showed that students were positively perceived HoM. The Pearson measure value was +1.13 logit, meaning that it showed the tendency of agree. However, some extreme findings were found from the person misfit. In terms of the students’ DD during this Covid-19 pandemic, the data showed that most students were frustrated in joining the English online classes. Unclear directions from teachers were one of the problems that stimulate students’ DD. From the perspective of HoM and DD, students were grouped into two when learning English in the pandemic: (1) those willing to improve their condition independently; and (2) those who did not care and had no initiative to find the solution.