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Although trauma-focused cognitive therapy for PTSD is effective and recommended in international treatment guidelines as a first-line intervention for PTSD, the psychological processes through which this treatment drives clinical improvement have rarely been investigated. The aim of this thesis is to improve our understanding of how cognitive therapy for PTSD works by testing predictions made by Ehlers and Clark's (2000) cognitive model of PTSD in two large datasets of patients receiving cognitive therapy in routine care (N₁ = 330; N₂ = 343). To increase the transparency and reproducibility of my work, I developed research software tools that help implement the methods used in this thesis in a transparent and reproducible way. I used bivariate latent change score models to test whether changes in the PTSD symptoms are preceded by changes in theory-derived cognitive processes and coping strategies during treatment. The results show that changes in PTSD symptoms were preceded by changes in negative appraisals, flashback quality of unwanted memories, and unhelpful responses to intrusions, but not vice versa. The relationship between changes in trauma memory disorganisation and changes in PTSD symptoms was bidirectional. To investigate sudden symptom improvements during cognitive therapy for PTSD I developed the R package suddengains. First, I examined how cognitive factors change before, during, and after sudden gains in PTSD symptom severity. The results indicate that sudden gains were accompanied, and to a smaller degree preceded, by improvements in negative appraisals and flashback quality of unwanted memories. A second study extended these results by exploring improvement in individual PTSD, depression, and anxiety symptoms during sudden gains in total PTSD symptoms. The results suggest that patients experience different patterns of sudden symptom improvements, while showing similar overall treatment outcomes. The studies presented in this thesis contribute further evidence supporting predictions about maintenance factors and clinical recovery during treatment by Ehlers and Clark's (2000) cognitive model of PTSD. This thesis also contributed to clinical research methodology by developing research software that facilitates reproducible analyses as well as a collaborative evaluation and further development of methods evaluating processes of change in psychological therapies. Overall, this thesis supports interventions targeting the identification and modification of cognitive and behavioural processes in PTSD.